With Edge, MS decided to re-implement some stuff through their own library. I don’t have an exhaustive list, but one particular thing is that for a while, SubtleCrypto (used for various operations within JavaScript) was present, but some mandatory algorithms were not available in Edge while they worked fine everywhere else (and maybe even in the non-chromium based Edge, which I don’t remember testing).

So, yes, there are differences beyond the integration of MS services. They are unlikely to matter to most people, but for dev it does reintroduce some weird quirks, as MS does.