But the problem also is that there is too many targets for a single company to destroy in a timely manner.
Like in a front thoudands of kilometers in length, there are hundreds of HQs of different command echelons along with all other targets like signal units, communication units, etc... and eventually after losing a few times to Astartes the enemy may learn to adapt. Like focusing everything on not allowing any Astartes force make a safe landing by blowing their transports out of the sky with anti air missiles and aircraft of their own.
And a single planet has way too many political centers for a single company as well.
Modern Earth for instance:
200 countries and that means 200 national level governments with each national level government having multiple locations like White House, Congress, SC, etc... and all the other agencies like Department of Defense with their own premises, etc... And then there are the state and city level governments of the world. We're likely talking about tens of thousands of targets at minimun.
And again there are thoudands of R&D labs across the world. Some of which are located underground in hardened bunkers.
Which is why I think the more realistic size for a Chapter would be a million Astartes. That means a Chapter could deploy a hundred thousand Astartes which when you minus the support staff would come to around three divisions or a hundred companies.
With this kind of amount of companies, they could conduct strikes at large enough and quick enough intervalls that the enemy would not be able to come up with a counter attack plan.
I think you're still missing a few details. They don't need to kill every single leader, torch every lab, and cut every phone line to win.
Let's go back to WW2. Let's say the nazis have those super commandos I was talking about, and they go out, kill the main generals on the allied side, wipe out the white house, 10 downing street, and wherever Stalin and his people hung out, blow up a couple ports and railyards, and destroy the Manhattan project, all in the space of a few days.
Now, that's not going to break the allied war effort all by itself,but it will buy time for the field armies to push back, will cripplied the allies ability to coordinate their efforts and maneuver thier forces. And the nazis can just do that again and again and again to keep the allies off balance.
As for stopping them, it's not very easy. Astartes are, above all, fast, and deploying the sorts of weapons needed to take them out takes time. When that sort of weaponry exists in the first place. Remember, on of the reasons marines favor deploying via drop pods and jump packs is that it's really hard to shoot them down (ditto for marine aircraft, which are fast and heavily armored, specifically to make high risk insertion easier).
As for million man/hundred thousand man strong chapters, that's a no go. For one, that's actually not enough marines, even freed of the current political restrictions on thier size the imperium couldn't field enough marines to have more than a handful of chapters, and they need far more than that.
And of course it's also way too many marines, as the imperium is not willing to allow such a powerful, independent force to exist, regardless of how effective it might be.
But there are plenty of ways to take out large swaths of Astartes. Heck while they're landing just send a nuclear tippped missile to their transport ships path.
Or use tac-nukes on ground against them.
Or massive artillery barrages.
40k does not have a lot of tactical or strategic nuclear weapons lying around, and those that they do have are not able to be deployed swiftly enough for this to work (specifically so that what you're suggesting cannot work, actually).
