Yes, but if Notion actually did allow compound time on separate staves it would take the music notation world by storm.
It can be done on a single staff now.
Set your time signature in either ¾ (6/8) or 9/8, then subdivide your bar measures to create poly rhythms.
9 bars of 6/8 would equal 6 bars of 9/8. Accent your 6/8 bars as 3 /4, and create the patterns you prefer.
No doubt though, it would be nice to set it up on two staves. Compound time signatures, e.g., 6/8 + ⅝ would also be nice.
Think of the possibilities! In fact, let's make this a feature request.