DCA's building was purpose-built for the Mermaid ride. The Palace of Fine Arts rotunda was kept from the Golden Dreams days, but the building itself is brand new and was built adjacent to the existing rotunda. The rotunda only serves as an open-air entry way, and serves no practical/structural purpose for the attraction. When the space was used for Golden Dreams, the building only contained the theater, and was completely separate from the rotunda; none of the theater building was retained
The MK building, on the other hand, actually reuses a couple of the walls (north and east side) from the old 20K building. If we're saying that one park had to work with an existing building, MK fits that bill more, though both buildings were essentially new I'm not sure why this was done, but I have to assume it was something related to ease of getting permits for modified structure instead of a completely new one. If you look at the historical images on Google Earth, you can see that the walls stayed there, even after the 20K building was demolished
But more importantly, I think the real trouble is that they decided that both rides needed to be identical, and therefore had to create a design that would fit in both locations. Had each park used a similar-but-unique configuration, I think they could have used the available space more wisely to get some additional scenes in, rather than using the one-size-fits-all approach that we ended up with
