I switch between guitar and bass a lot so I like low action on my bass fret board (especially when I'm trying out jazzy bass solo improvising). I play mainly with fingers.

If I forget about what my right hand is doing while I play something fast or difficult, I start fingering/plucking the strings in towards the body, rather than parallel across the body if that makes sense.

With my low action, the strings (especially E) start going THWAK//THWAK//THWAK, though the notes still ring out properly and it can be EQed out.

Should I
1) Compensate by raising the action (possibly making switching between guitar more awkward).
2) Ignore or EQ it out.
3) Concentrate not to pluck strings in towards fretboard.
I'd just raise the action. You don't want to forget that bass and guitar are two different instruments haha.
ESP Custom Shop 40th Anniversary Eclipse
ESP Standard Eclipse-II
Ibanez AF85VLS
My bass does this too, but I think it's worth it considering the comfort you get while playing. When playing I barely notice it.

So my advice would be to ignore it, and play how you like.