I vaguely remember a forum forum thread about that “soldermask only on copper, not on not-copper areas”. I think you will get no relief with kicad v9.
Regarding selection by markings - this is only for searching or can you search and indicate to change the assigned footprint massively?
Depends.
symbol fields table: Here you can bulk-change the footprint assignment.
search panel: this also allows to select the wanted symbols. Sadly it’s currently not directly supported to change the footprint assignment for a selection of symbols.
A workaround is described at the end of this thread: (Change selected components footprint - #11 by gschelotto)
already open gitlab issues which may help in your workflow (if implemented sometimes):