I'm not saying that Picard stepped foot on the E-D and said he hated the carpet and wanted it all ripped up or the corridors replaced, or anything like that. (However, based on crew quarters we've seen from TOS onward, it's clear each person has relative free reign over decoration. Look at Spock's quarters.) But when it comes to the control center of a ship that's going to be on an extended mission, I think it makes sense to have some Captain's discretion.
I don't really buy this explanation. It seems like a leap to think the major driving reason behind why bridges within a class have different features is because the captain wanted it that way.
Given the fictional nature of Starfleet it's hard to know how things like ship assignment works, and I'll admit to a certain level of ignorance on how the real Navy does it too, but I'm willing to bet dollars to doughnuts that a captain is assigned to a ship well after any decisions about bridge layout and construction are made. If keel-owning captains got a say in the initial ship's design, then how far would Starfleet go in terms of materials and manpower to reconfigure a bridge just because a new captain wanted something a different way?
What we do know about 24th century bridges, at least the Galaxy class ones, is that the stations are mostly task-neutral. So if a captain wants her tactical officer up front on the left and her science officer where Picard had the Conn she could do it that way. But that's not the same as saying captains can make decisions about where hardware is installed.
I'm sure that captains are constantly required to send feedback to fleet engineers about the effectiveness of their ships' bridge design and such feedback will be evaluated and incorporated on future refits to ships of the class as they are scheduled or incorporated into new construction as it's ordered. That'd be my guess as to the in-universe reason we'd see ships of the same class with different bridges; one might have a tech package the other doesn't, have completed a refit the other hasn't, or has had a different system installed from the get-go for comparative performance analysis. This is, I think, pretty likely when you look at the Yamato vs. the Enterprise D.
