Oil filter bypass valves can be: in the filter; in the head; in both. I am not aware of any spin-on engine oil filter that does not come with a bypass valve as part of the filter itself. Of course, there may be exceptions but the Baldwin B95's, for example, which are a common spin-on for these engines DO have bypass valves and I'm confident that any equivalent filter would.
An engine that originally came with a cartridge-type oil filter will have the bypass as part of the head assembly. An aftermarket spin-on head MAY or MAY NOT have a bypass valve. SO...if a spin on is plumbed to the original cartridge-type oil filter head, there may be two bypass valves; if a spin-on is attached to a head WITH a bypass valve, again, there will be two, one in the filter and one in the head. If the bypass in the filter is activated, oil is still flowing in the filter canister, just not flowing through the filter media. If the head bypass is activated, oil is not flowing to the filter. THAT was the thing I was thinking about. If there is a bypass in the head and the filter, a clogged filter would activate whichever bypass spring produces lower pressure. Bypass valves are typically opened anywhere from 7-20 PSI, depending on the spec for that filter or head.
Frankly, it's unlikely that a filter head bypass valve would be partially clogged and I can't really imagine how that could happen. If it did, there would likely be a noticeable oil pressure difference between the engines as they were quickly revved up. One engine's pressure indication would tend to lag the other as the revs came up though they would probably both be fine at normal cruise. SO I'd hazard a guess now that changing the filters ensured that a plugged filter was NOT causing the temp difference due to a filter-head bypass activating..
Just to ensure...verify again that the engine coolant temps are essentially the same on both engines with the IR gun shooting both thermostat boxes on each engine (total of four) and that all four are reasonably close in temp reading.
I have no other idea at the moment as to what could be causing the temp difference AT THE FILTER. Frankly, absent the possible bypass issue or some sort of radically different plumbing on one engine compared to the other (much longer oil hose, oil cooler in one/not the other, oil cooler clogged in one, etc.), I am clueless!
Interesting mystery!