Seems like I always see things differently. I think sealing around the pipes through the plywood sub-floor is not very useful, and maybe harmful.
1. Some air return from the belly is necessary for the furnace to efficiently send more hot air down there. Some of those oversize holes are the air returns.
2. The duct from the furnace that goes down into the belly pan is a flexible duct, just hanging down in the belly with an open end. Any mouse that gets into the belly can find it's way through the duct system to the air outlets and into the interior. Or, a mouse can easily chew through the flexible duct at any point in the system.
It make sense to me to seal penetrations of the exterior belly skin, but not the sub-floor
2014 Silverado 1500 5.3L maximum trailering package (yes, I'm towing the 34')