@User: I am not seeing those issues on rc5 (develop).

Circuit 1 contains 1883 devices, Circuit 2 contains 1883 devices.
Circuit 1 contains 1426 nets,    Circuit 2 contains 1426 nets.

Circuits match with 1 symmetry.
Resolving automorphisms by property value.
Resolving automorphisms by pin name.
Netlists match with 1 symmetry.
Circuits match correctly.
Result: Circuits match uniquely.
Logging to file "/openLANE_flow/designs/zipdiv/runs/lvs_issue/results/lvs/zipdiv.lvs.log" disabled
LVS Done.
LVS reports no net, device, pin, or property mismatches.

Total errors = 0

However, I am suspecting that sometimes something goes wrong with OpenPhySyn's pin swapping algorithm, but I can't seem to catch a test case...