I’m definitely not a big fan of the idea of doing this on a filter-by-filter basis:
Practically, that would mean adding a new option to the filter parameters to allow saving the output layers as separate image files, instead of output regular layers.
This is possible, of course, but more broadly, this also means:
If we do that for that particular filter, we should also do that for any filter that produces multiple output. Otherwise, I’m pretty sure someday someone will ask the same feature for another filter.
This would make these filter interfaces more cumbersome, for the only reason one the Paint.NET plug-in doesn’t manage multiple output.
Clearly, if the Paint.NET plug-in cannot easily manage multiple output layers, then it has to provide an alternative solution, that is global, and that can be applied on all filters that produce multiple output. Maybe Nicholas Hayes has a suggestion about this, but in case of multiple output, maybe it could open a file dialog where the user can chose where the output layers are saved. But this has to be a global solution, not a filter-by-filter hack.
EDIT: In any case, only Nicholas can do something about it, as he has developed the Paint.NET interface to G’MIC-Qt.