Even though I don't use my Multigraph for printing on graded papers, but with VC papers, I do use it offen to expose enlarged negatives for Pt/Pd, so I have some personal experience on how to use it without the filters concern.

Your second opinion seems OK, so that you can choose a separate channel and for example contrast grade #2 in that channel and adjust the yellow and magenta filters to zero.

You can always use the probe to find out the proper exposure time for your negative and paper-developer combo, and for the magnification changes also naturally.
You can keep this channel for your preferred paper and developer, and for differences from batch to batch of paper(it happens) you can make the small adjustments on the "adj.cal" settings.

Hoping that this helps,
Best regards
Mehmet Kismet