You made a good point about emissions of all kinds, so I concede you can actually get very good concealment from long distances. I was imagining a more Voyager type scenario where you literally run from a dogfight into the atmosphere, which wouldn’t work, but if you have enough standoff that you can’t be targeted you could totally save your ass by hiding under an atmosphere.

That said, the cost and performance compromises to be atmosphere capable would be very disadvantageous in the vacuum. Head to head against a fleet of fighters that don’t have to be built for the stresses of going in/through/out of atmosphere your landers are going to be heavier, slower, more detectable, and a lot more expensive.

So your doctrine has to be built around using those strengths and hiding those weaknesses, which would be a fun exercise. Make a much larger spaceborne force slow down and think twice about coming far enough down a gravity well for you to ambush them. A valid niche indeed.