Nobody should fault you for the foundry limitations.
alas thats not the case, people have marked me and others down for foundry limitations all the time. people have complained because mission are too linear, offer few rewards, or because of foundry bugs. none of which i can do anything about. some people even mark me down because im english and i use english spelling on some words.
you can either a) ignore them or b) try to avoid some of these issues as best you can. the bridge thing is a risk that some people will pick you up on.
now i personally would not have a real problem with someone using a generic bridge. it would be annoying but i would never mark someone down for it, as i accept there are limitations and i appreciate what the author is trying to do, but some people will not see that and just mark them down.
if an author really cares about his rating and wants to please as many people as possible then i would say avoid using the whole bridge things (or just to the ready room bit as a compromise) as i guarntee wit will affect the score.
if you are not as concerned about ratings (and personally dont be, as you can never please everybody), then go with the bridge and tell the story you want to tell.
I , generally, do not use bridges in my missions simply because I don't like the limited selection, but that's just my opinion. I'd never be bothered by playing a mission where the 'story' bridge is different than my own. Afterall, I'm in it for the story. That being said, not all players are. Some don't even want to read the dialogue. I tend to write alot of it in my missions and create characters. I've had reviewers complain that I put crewman on their ship that they don't have. It is sometimes a necessity for the story. Some will say "I like the relationships between crew members." and the very next review will say "I gave you 3 stars because I don't have a Ferengi Transporter Chief on my ship."
You'll never please everyone. Star Trek has always been successful because it's character driven. So, without the characters, there isn't a story. In that spirit, you could say that the bridge is a character in the story, as well. If you feel you need it to tell the story, than use it. If the player is willing to suspend disbelief, a prerequisite for Star Trek to begin with, than you'll be ok. It would be great to write the perfect mission, but that is not possible. So just pick your priority. I, myself, would worry more about plotholes than whether my character's uniforms are going to match the player's. Again, this is just my opinion and everybody has one.
You know when I signed up as a reviewer I was worried about this kinda thing. I even put something into a review of Levithan99's story because the Borg were able to shoot me through the wall before I got the code to open the door they hid behind. I did not mark him down for it but I did mention it. This while I am trying to be careful to not mark a creator down for things that the Foundry places beyond their control.
What I am saying is it is all well and good that you would not mark a story down for using a bridge that was not the players, as fellow creators aware of the ins and outs it behoves you to do so. Where the reviewers who may not have made a story yet, like myself, are unaware of the medium's limits just might.
Because the majority of reviewers and players are unaware of the limits of The Foundry it might be best to use workarounds as often as possible. That much said, to me the story is far more important than the set so I would not be inclined to mark a creator down for it. If you have to then do it but, (and I am sorry to say this), be ready to take your lumps. There are some myopic reviewers out there.