If I here correctly it sounds like AE is more time-centric, not frame-centric.
One workaround is to render out the 48 frame 25fps sequence, then re-import and interpret the footage to 23.98. Voila, 23.98 48 frame sequence.
Explanation: I am making 23.98 and 25fps versions of an animation. The edit is different for each, 48 frames for 25fps, 46 frms for the 23.98. So in both, this shot will be 1.92secs. I was hoping to nest the 25fps in a 23.98 comp and trim the last 2 frames.
Maybe my explanation helped. Just looking for the correct/cleanest was to do this. Rendering out and re-importing seems silly.