additionally to exploded mesh and substances methods, if you are using toolbag you just separate into different bake groups.
You could also pull the UV island you don't want involved outside the 0-1 space and reinsert it afterward. This may not accomplish exactly what you are asking but it's pretty vague what you are asking.
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There's "match by mesh name" in Substance:
https://support.allegorithmic.com/documentation/spdoc/matching-by-name-127074308.html