You could try ,
Shorter motor bolts , or washers under the bolt heads .
My opinion would be that , no , they won't run in and become cooler by themselves.
Am presuming that it's just the two new motors getting hot - are they defo exactly the same motor ??
(Motors without props will run hot , but youlld think it would be even )
Lowering the d term can help with hot motors but can't see that that's relevant here.