In the process of using model.loops to identify regions that I will need
to model in a multi-chain situation, I have noticed that it returns
insertions between chains as a single loop.
If you don't want it to do that, set include_termini to False. (It would
also be pretty easy to write a function to split loops in the way you
describe too, although I think it would make little difference to the
loop modeling algorithm other than a different starting conformation.)
I can't run your test case because it looks like you've confused two
examples (5xki vs. 2abx).