For me personally (and there could be other usage scenarios than mine, of course), adding a Dimon option would be the simplest. How Dimon passes the information to to3d is normally hidden from me, so it makes little difference (for me).
In general, I think it would be also helpful if Dimon, when it detects a discrepancy between various sources of slice distance indicating overlapping or thin slices, notified the user and presented options. Or to3d could do that, but because users are encouraged to use to3d via Dimon, probably Dimon is the better place to do it.
I mean a notification like many AFNI programs do: one that comes to mind is 3dAllineate which warns for lack of -cmass when it thinks it would be effective, or adds -autoweight (I think) if lpa or lpc is used, and tells the user it did so, and tells what other options are. Just a suggestion to make life easier for users who may not remember all the intricacies of AFNI programs.