The mush-room space-dock from Kirk's era is able to accommodate a Galaxy class ship without problem to my knowledge.
It certainly has the interior to do it.
Although, by the 24th century, it's possible that SF removed the internal central section entirely (the one which divided ships locations) or they could have retrofitted it to accommodate the Galaxy class itself.
Either way, I don't see a problem with having a larger mushroom type space-dock in the first place.
The design itself is probably sound and modular enough to accommodate upgrades for several centuries if not a millenia (and SF engineers find a way to upgrade outdated technology all the time).
The larger mushrooms could be located outside of SOL and might have been constructed while the Galaxy class was still on the drawing board (or was even proposed as a design).
There are a ton of options to ponder on.
One would also have to take into account the fact that building technology is highly advanced in the 23rd and 24th centuries.
They would probably use transporters and replicators extensively for industrial purposes (not to mention automation).
I doubt any SF ship would take more than several months to be constructed (6 months tops for the Galaxy class).
Maybe in the 23rd century it would take them about 10 to 20 years to construct a mushroom spacedock.
In the 24th, they would probably have the design handled so it would take at least half as much.
The Delta Flyer for example was constructed in less than a week (although at first, Paris mentioned it would take 7 days).
So, if we take into account that a crew of Voyager (with their limited resources) took a week to build something as big as the Flyer, my theory is that an actual drydock at Utopia Planitia (or any other construction yard in general) would probably need half as much time since they have specialized equipment and virtually unlimited resources.
A Galaxy class being constructed in 6 months time seems realistic ... perhaps even less if there would be heavy replication involved.
5 years for construction of something as large as a mushroom space-dock seems like an attainable goal.
If not far less.
The Federation IS comprised of over 150 member worlds.
If we take into account that all of the member worlds would have their own construction facilities (and they would have to have them because those planets would have created their own ships prior to joining the Federation and would undergo upgrades to keep them up with advancements), then it stands to reason one can complete the work in question in far less time if you give each member world a section of the space-dock to create, which would be taken later on to a specific location.
One can easily churn out a whole lot of these stations in a much shorter time frame than say 5 years as a result (especially if it's constructed in say 150 pieces and then towed to a specified location where it would be assembled).
That's a good way to look at it, I think, and they're all good and valid points.