I appreciate that gameplay comes before realism, but any arguments about new player expectations should come from real-world logic. So why not apply some?
It makes sense that for a door that opens quickly, the attackers should have the advantage since the person opening the door can perform a count-down to indicate when the door will open, which the defenders have no idea about. Even if they have cameras on the outside of the ship, they may not see, or correctly understand, the signal given from the door opener to the rest of the attackers as to the timing of the door opening.
A door that takes some time to open (like the blast doors in Star Wars) effectively loses the initiative for the attackers and puts both groups on equal footing. For example there's a big clunk before any door movement, alerting everyone, then the door slowly opens.
Assuming reaction fire is what it claims to be, therefore in the "small door" scenario, the attackers should get a reaction modifier bonus, but this would likely mean that the attackers with highest reflexes get a couple of shots off before the defenders highest reflex guys can return fire. In the "large door" scenario, the attackers just don't get a bonus, so highest reflex wins. Note that if the player wants to turn off this reaction fire for their attacking team, they should be permitted to do so in order to be able to use their TUs as they please. "Hold fire lads, only shoot when you've marked a target" kind of thing.
The defenders not having a way to remotely open or close a door on their own ship is ridiculous. Even if we assume that because of there being aliens out in the field, they do not lock the door, they would have a method of opening it remotely, locking it open, and locking it closed (although perhaps the latter would be bad for gameplay if the player had brought no breaching devices). Assume that in order to access the door, the attacker has to hack it, and that it takes longer than a normal door open. Once open, the door cannot be closed by the attackers as the hack has destroyed the mechanism. The option to open should not be "open", but "hack".
If the door always closes at the end of a turn, it should be the alien turn, and one alien should have to spend some TU to do it.
With normal (non-alien) doors on the rest of the map, door spamming is a legitimate tactic, in that you could do it in real life, but it should trigger aliens to use explosives or heavy weapons to blow the door (and the door spammer) away. Any character opening a door themselves should get an aim penalty if they shoot a two-handed weapon in the same turn. They are moving their body and not steadying their weapon.
I would also point out that the TU cost for opening a door implies that someone is actually DOING something. If we're agreed that it's hacking, then fine I could buy that a larger door has more security so hacking has a higher TU cost. If we're talking about pushing a button, then it's silly. The button-pusher should not be penalised in TUs for a door being slow to open once initiated.