Drewi: I have been working with this rig and have come across one problem, in so far as monopeds!
If I use the two legs as a starting point for skinning, then that causes some problems, so will redo the Rig with a set of Tail bones to overcome the problem. We can leave the biped bones intact but not used when skinning.
You are right regards the stumps bases, when the three models are collated there is always some conflict in scales and in most cases the scale of each object must be adjusted to fit with each other ( Does that make sense!?)
I`ll redo the rig and post a revised one to dropbox when ready!