This reads a bit like the dismissal of SQLite comes down to a desire not to do any data modeling at all, which seems a bit silly in a discussion about standard formats and schemas. Obviously you shouldn’t put your data into a single hard coded “column per feature” table. So the limitation of “only” 2000 columns is really just there to nudge you in a better direction.
You put it this way because that's how you usually train models. If you don't train models at all on your data, then for sure you don't need to care about such limitations.
