Tried it and it seems to work just fine. I took our smallest part (one that is most likely to move around on the magnet) and tried it with
1) the way we currently do them (roughing pass and finishing pass as mentioned earlier)
2) my very nonelegant way I mentioned earlier
3) 3d engrave with three tabs
4) 3d engrave with two tabs
On these particular parts the three tabs wins (but is less easy to remove than the two tabs).
I think I tried every tool path option except for engrave.
I will keep testing this way.
I still prefer stevespos way because I don't have to manually edit the parts (adding the actual toolpath and tabs), but if I (we) can't get that way to work, this way should do the trick.
Thank you again for your help.