The ship being under thrust wouldn't particularly have an effect on the sense of gravity unless the ship's inside is oriented so that the floor points towards the thrust vector.
I can't be sure whether that's the case or not, but it seems unlikely if you look at the layout of the cockpit. Alex looks straight out the window in the direction that the Roci moves. This means that the thrust vector is behind Alex, not below him. If the ship were to suddenly start accelerating, Alex's head would be pushed backwards (like in a car), not downwards (to simulate gravity).
Since his chair is perpendicular to the floor, that means that the floor isn't oriented towards the thrust vector. The crew would be pushed sideways instead of downwards when the ship accelerates; similar to when you stand on a bus and it accelerates or brakes.
Caveat: If the cockpit's floor is aligned differently from the rest of the ship, then it might be different in the hold. However, it seems very impractical to orient floors in different way, especially if you want to rely on a uniform gravitational direction.
Answer: Assuming the Roci isn't specifically aligned for it to happen (which seems unlikely given the layout that I've seen), the ship's thrust will never be able to simulate gravity (towards the floor).
So your question is making a wrong assumption.
However, I think there is more to answer here, to maybe address your confusion.
Even when they are travelling, they will be coasting (no thrust) for considerably longer than they will be accelerating (under thrust). Going by current spaceflight, the idea is that you quickly accelerate up to your desired travel speed, then cut the engines and coast at that speed (this does not cost any power (or thrust) since objects in space do not slow down).
Although it could be possible that ships operate under continual thrust (e.g; if power consumption is no issue); but there are several scenes in which the Roci is flying stealthily (= no engines) where you can still see the crew bound by gravity (or what looks to be gravity).
In all of these cases, the mag boots explain why the crew is seemingly bound to gravity, even when there is no scientific reason for gravity to exist in this context.
Everything that is not bolted down on the Roci works with magnets. This includes the cargo crates (this is relevant to the plot in the S2 finale episode), the mag boots, and everything else I've seen.
I am omitting little things like handheld devices or personal items, I assume there is an established explanation for what happens to these items (where they get stored), but the TV show simply does not have screen time to showcase every little detail about space travel.
You can call this a "cheat" for the showmakers to explain away little inconsistencies with gravity, but it makes sense for them to do so. The characters continually being in zero G would not only be expensive to film, but it would be a distraction to the viewers and it wouldn't add anything to the narrative (other than meticulous scientific detail). The costs outweigh the benefits here, in my opinion.
Mag boots are an acceptable explanation, and I have to admit that even with the mag boots, they have still added plenty of scientific detail about how they work; instead of them becoming a magical gravity device.
But this is the answer that encompasses most scenes without zero G that also lack an explanation for why there is (artificial) gravity.