Sadly I read that as "Other tools do their own thing so we decided to do our own thing too" :(
Though admittedly, "convenience for users" is a rather tricky thing to define, as you really need to define "which users". I imagine ~/.projectname is easier getting started out, but the long term management is why we (try) to have standard locations for things.
> Since 1995, the team's member, Jun'ya "ZUN" Ōta, has independently developed programming, graphics, writing, and music for the series, self-publishing 22 main titles as of August 2019.