I don't see the difficulty of the taking off under fire situation either.
Firstly, I maintain that even moving the 'blue circles' to an airlock area at the top of the steps that fades you into just inside the cockpit would improve the immersion, fit the narrative, avoid the need for modelling any more ship interiors and add almost no more 'vulnerable time' than currently exists. The gap between the pilot's chair and the Armstrong Moment 'Circles of Laziness' is a poorly considered designed in gap. It actually has next to nothing to do with Ship Interiors as it's normally described. It's just bad design and lazy programming and the gap should be plugged, it's a simple as that. After all, why run to the settlement - you could just teleport there. Why take the lift to the concourse, you could just teleport there. Why bother with the Witchspace animation, you could just teleport between stars. Why fly to a planet, you could just teleport there.
I repeat, the blue circles are a designed in gap in the narrative that is simply because of laziness. That gap could be, and absolutely should be, located where it makes narrative sense to locate it. Not hovering above the dust next to the access stairs that you are actually prevented from accessing. It a sign saying 'this way' next to a sign saying 'no, this way not that way'. And it's designed like that! It's not good enough.
On the escaping under fire situation I think you just have to consider how it would work if you were actually there.
I don't think you should be able to take off unless you're strapped into your chair. That throws up all sorts of physics issues, isn't necessary and in most cases makes no sense no matter how much you can shout 'Get us out of here Chewie!'. So you have to get from the stair to the chair, perhaps while under fire. In terms of gameplay this is no different really than getting from the base to the ship.
In the 'real' world, you get into the ship and close the door behind you. No combat within the ship required. You either have you ship's automatic defenses doing their best to buy you time by returning fire, or you just have to hope that your noble steed can absorb the hits for long enough to give you the time to get back to chair. If this is an overlong journey past the onboard pool and giftshop, well, you brought the wrong ship and you're going to die.
Assume though that you're legging it down corridors. Dramatic music is playing, sirens are sounding, red lights flashing, your ship's computer informing you in its anodine voice that unless you get back to the chair in ten seconds you're going to explode in a painful and messy way that will seriously affect your resell value. Sparks and jets of gas are shooting out of random panels of your beloved ship with no logical explanation, as you try to get desperately back to the cockpit in time, cursing yourself that you parked so close to the base, and why oh why did you bring the Winnebago, when the quad bike would have you got you away quicker. Your ship won't take off without you in the chair, as the forces could be fatal and the inbuilt safety systems won't permit it. Fortunately, on this occasion, you'll get away on time, but having taken a bunch of damage. Next time, you'll park behind the hill and sneak in on foot!
I don't see the gameplay downside, the programming downside, or why it couldn't be done step by step. At the risk of sounding like a broken record though, get the blue circles up out of the dust most importantly, the rest may or may not come later. If it comes it could be an awesome extension of the base attack gameplay loop without needing to become Fire Extinguisher Simulator. So many ways it could be done.