So far as I know, only FASA makes that distinction. Indeed, TNG goes out of its way to describe the LN-64 engines as pretty much identical, and, of course, CODA and ICON both treat them as such. (And, for TOS, FJ specifically listed each class with the same engine).
Since we do see engine types that are different for different ships, such as the USS Grissom, SS Aurora, etc, seems to me that different housings would mean different engines. Add to that that specific components of the engines are VISIBLE in each configuration, and it strikes me that an LN-64 is an LN-64 is an LN-64.
TAS established 'similar engines' like the PB-32S, which is structurally the same, but smaller and with lesser power and 'coil space', effectively. Basically the difference between a V-4 and a V-8 configuration. Same overall tech, but less of it. THAT idea I can see a lot easier than the LN-64 housing for 25 completely different engine designs!
Besides, gives me an excuse to unveil a couple of late 2260's engine housings that way. ^_^