Unfortunately, the lore behind plasma weaponry is pretty sparse, so all we can do is by conjecture based on examples and what we know in comparison to other weapons/armour types.
Okay, bit of rambling stream of consciousness here:
All that's really known is that the Brotherhood initially reverse-engineered and produced cruder and more limited copies of Scrin weaponry for use in their Cyborg Commandos and Banshee units (later abandoning them in favour of charged particle beam weaponry and tried and true lasers), that they're tiberium-fueled in some way, and that the Scrin use them extensively and without signs of limitation on their ammunition or rate-of-fire.
A flight of three Banshees were capable of downing a Mammoth Mark II, however, indicating that GDI armour technology at the time was incapable of resisting plasma weaponry (or at least the Brotherhood's crude approximation of it): The Mammoth Mark II was also shown to be resisting, without any issue, the laser strikes of a second generation Obelisk of Light; the first generations were shown to be able to completely destroy light vehicles and main battle tanks in a single shot.
So, it appears that GDI metallurgy and armour technology during the Second Tiberium War was strong enough to resist Obelisk strikes at its best (while their mainline forces, like the Titan, being carved up like a turkey at Thanksgiving), but not enough to resist cruder plasma weaponry.
There must have been a hell of an upgrade in the next seventeen years, though, as first generation zone armour pretty much doesn't have these issues (see below).
Nod flame weaponry is a bit contradictionary in the sense that the designers behind C&C (the later games anyway) didn't do their research: The upgrade for the Black Hand subfaction is Purifying Flame (~2030's in-universe), that uses a "tiberium-carbon" blend for fuel and turns the flames 'blue' and 'hotter'.
Even ordinary flamethrowers used in the Second World War were roughly at 3000 degrees as they were deploying, and the flames were, well, yellow. Nod's flames were also yellow, indicating that the temperature was at least 3000 degrees (and this is with conventional fuels, not including whatever exotic bullshit they came out with due to tiberium) on their flamethrower tanks and infantry during the First and Second Tiberium Wars.
So, for the flames to turn "blue" indicates that they must burn hotter than at least 3000 degrees.
The issue is that Nod, even up to the events of the Third Tiberium War, didn't adopt the Black Hand's Purifying Flame as their default flamethrower fuel for their mainline forces. Their flames are still yellow.
As you can imagine, this creates a bit of a paradox as zone armour was designed to be able to resist ion storm lightning strikes, as they're expected to go into Red and Yellow Zones! If we go by real-life physics by using examples of lightning bolts (which are instances of charged plasma), they can reach 20,000 degrees... per strike.
Hell, ion lightning may even be hotter than plasma weaponry: We just don't know. What we do know is that ion lightning destroyed the Kodiak in a single shot (Firestorm's introduction FMV).
Does this mean that even first generation zone armour types are pretty much immune to Nod flamethrowers, if they're at roughly 3,000 degrees, given they're designed to resist ion-charged lightning?
Are Scrin plasma weapons far below 20,000 degrees, so they're inferior to lightning bolts? Do they match it? What temperature reaches do the Purifying Flames push to for them to become black and not violet or something? Either way, it shows how tough and advanced the first generation sets of armour are because they're designed to brave ion storms.
Would more far more advanced and refined versions of Nod's plasma weapons used by the Scrin... which disabled a Mammoth Mark II in a single passing run (depending on how hot the Scrin's plasma weaponry can be per strike), be more or less effective?
But, back to flame weaponry used by Nod: This all indicates a logical dissonance that can only be resolved by either a) there's something more to Nod's flame weaponry that we know nothing about, which is likely due to tiberium being an influencing factor or b) the designers behind the games didn't do basic research or maintain world-building consistency in this aspect.
However, the games own intelligence/lore database for GDI says that Nod Flame Tanks are unable to penetrate the crew compartment of GDI's armoured vehicles, such as the Predator and Mammoth Tanks -- so, GDI armour technology/material by 2047 can withstand at least 3000 degrees of sustained fire (no pun intended).
What we do know is that by the time of the Fourth Tiberium War, however, the Nod Separatists (and later mainline Nod) modified their Third Tiberium War flame tanks to be able to burn/destroy GDI zone armour as they were, in their default state, unable to damage the latest generations of GDI zone armour. They were pretty much completely useless.
So, first generation zone trooper armour was designed to be top of the line and the forefront of armour technology (GDI's R+D focused heavily on them as they, along with things like sonic emitters, were key to their anti-tiberium agenda, which had become the focus of GDI by that point). Does that mean they have the same resistance armoured crew cabins on vehicles had, given GDI's metallurgy capability at the time?
Going by the Trail of Flame ability lore, it's also said that the fuel aboard the tanks is inert unless used by the tank itself, meaning that shooting the fuel canisters and hoping they'd explode is a fool's errand. So, that implies that each tank is a separate chemical, with each being inert until combined; that tiberium bullshittery is in play; that the fuels are somehow just one chemical mixture in both tanks that are also inert until used by the flame tank.
So, following these trails of thought? It means that zone armours, even the first generation, may literally keep the wearer safe and comfortable from flames that are at least 3000 degrees hot, and are designed to be resistant to lightning strikes that are at least 20,000 degrees hot.
The newer models took this a step further: The Nod Separatists had to push their flamethrowers to well past 3,000 degrees to just breach the new armours. What temperatures did they have to reach? Does this mean that prior flamethrower weaponry was, in fact, capable of breaching zone armour? Or that they had to do this because of GDI's increasing reliance on zone armours, like forcing a square into a round hole as a solution?
Nod's crude plasma weaponry attempts were capable of breaching GDI's top of the line metallurgy and armour in the Second Tiberium War, which resisted Obelisks' sustained firing.
The Scrin's plasma weaponry is like comparing Nod's to being crude muskets while theirs are like assault rifles from two hundred years ahead in our future.
So, unless Scrin plasma weaponry is capable of surpassing or is equivalent to lightning strikes, zone armour is resistant either way to varying degrees of success, whether they're of a lower temperature/energy state (e.g. between 3,000, meaning pretty much great protection if not immunity, and 20,000 which would be an issue after repeated strikes) or not.
As you can see, C&C lore has its problems, heh.
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