Hi Phil,
Is this still an active issue for you? You raise several good points and I might be able to help with many of them. One thing that caught my eye was this:
> Presumably LVS is not flagging this as a comparison mistake because it already
> announced it would not compare some of the pins via the NON-IDENTICAL PINS message?
LVS should fail due to this, so you shouldn't be able to get a clean LVS, it just so happens that it's not reported as a "discrepancy" the way you might expect other kinds of connectivity errors to be reported. It should be reported like this:
# # #####################
# # # #
# # INCORRECT #
# # # #
# # #####################
Error: Components with non-identical signal pins.
A "warning" would usually allow LVS to be correct if everything else is ok but this non identical signal pin should be an error that forces LVS incorrect.
"Signal" is an important distinction here. LVS can issue a very similar message for "power or ground" pins and due to the way power and ground often propagate through the design with name changes along the way, differences of that kind can give a "warning" instead of an "error". The lvs power and ground name statements can be used to indicate which nets should be considered as power or ground rather than signal pins and you might control the behavior in that way if it works well in your flow.