I will take that over him just disappearing, and I like the breather personally, I think it needs that before ramping up for the bombastic finale and creates a much needed respite before going downhill.
Also I prefer the Assembly Cut opening because it is not quite as mean to the people in the EEV (and thus reflects better on Clemens' character), alongside just better cinematography.
As for which Chestburster, I think the Ox looks better (the setting, the imagery, religious undertones of it) but get the view for the Dog being more impactful... but only on a surface level... I would honestly argue that just makes the emotional energy of the scene all messed up, in the Assembly Cut I am focused on Ripley's grief, in the Theatrical Cut it's so distressing what happens to the Dog that I think the emotional focus ends up in the incorrect place.
The only thing I prefer about the Theatrical's the score not being messed up during the sacrifice scene.
I don't even really enjoy the Threatrical Cut, I can't tell you exactly why but it's just not the same to me, it's a combination of all of the above.