I believe that whether one uses ṃ or ṁ, there will be no undesirable consequences.
The reason I asked the question was because of search engines.
The Searchable Sanskrit Library has a search engine covering multiple collections so all anusvara's (like all other letters in it) need to follow the same convention (either overdot or underdot) . But it seems that since all the collections I've seen use m underdot thats been chosen as the de facto standard.
Thanks,
Harry Spier