This really is a major limitation. There are lots of great NAS/server motherboards. There are lots of great Mini-ITX motherboards. But there are few that are both–that form factor just doesn’t have the real estate to support that mission well. You can definitely build a NAS with a Mini-ITX board, but there will be trade-offs.
FWIW, the best (on paper; I haven’t used it) Mini-ITX board I’ve seen was mentioned by @Constantin in this thread (which has a bit of discussion of other options for a small-form-factor build): the ASRock X570D4I-2T.