I have done some more research and come to a conclusion of my own:
Fiber is not necessarily "backwards-compatible" as it depends on the optical transducers (laser and receiver) within each piece of MADI-supported equipment. There seem to be a trend in the industry towards 50/125, because a smaller glass core (50um vs 62.5um) reduces modal dispersion and thus allows for longer reach (see more here, pdf).
The situation is a bit of a two-egged sword, as most new, non-MADI equipment run on OM2 or OM3 (50/125) and some include backwards compatibility with OM1 (62.5/125). However, MADI equipment is guaranteed to run on OM1 (because of the standard), but might not support OM2 or 3. E.g. Avid has published information about their XLogic IO products claiming that their transducers are optimised for both OM1 and OM2 (see here, HTML). (Note that Avid claims that OM1 allows for longer distances, which must be a typo.)
So all-in-all, it doesn't seem necessarily straightforward. The bottom line is that it really depends on what equipment you eventually will put in, and what kind of fiber that that equipment has been designed to work with.