Should someone use a Nintendo Account to log in and play Pikmin Bloom, then they can’t later use say a Google account or account from another Niantic game to log into it.
People starting Pikmin Bloom for the first time might experience a connection issue depending on whether you use a Google or Nintendo account to log in.
As for why someone would want to link a Nintendo Account to Pikmin Bloom, there are exclusive benefits.
Both the official support page and initial reports note that starting with a Nintendo Account blocks you from using other logins.