Extra ?groove? in each tray section bottom

Post a photo of how things cut?

You are pocketing with a ball-nosed tool — better to do this with a perimeter pass (for the rounding) and a square tool for the balance.

The lines do show if you angle the preview a bit:

If you want a smooth bottom see:

Otherwise, to achieve what you seem to want you will need to leave the bottoms uncut, then nest a series of geometries to which you will assign a No-offset contour:

(adjusting the distance so as to arrive at an even distribution w/o a central point is left as an exercise for the reader)