In the case of bearing clearance, I would only trust plastigage because it shows precise clearance after torqueing the bearing cap to spec. Yes one can base clearance using stock rod/bearing specs and how much the crank journals were cut down, but humans make mistakes as well as bearing manufacturers. Plus, unless measuring instruments are calibrated, do you want to trust their accuracy to such a critical part of engine build? Not me! Plastigage verifies the theoretical clearance.
How would one accurately measure the ID of a connecting rod with the bearing cap installed and bearing shells in place?
Seal installed or not, it won't have effect on bearing clearance check.