This function assumes the user knows what he's doing, this is also clearly
stated in the documentation:
"RMSD of atom positions (taken blindly in the order in
which the atoms appear) in the two given views."
This check at least avoids a segfault when the number of atoms does not
match. The result would be completely wrong anyway...

Combination of reference_existing_object and RemoveChain can lead to segfaults.
Overhead of change is 1us per call for a test case with 18 chains. Hence it is
absolutely negligible.