Minor clarification: We didn't try reproducing the issue, but came up with an explanation.
Unfortunately that explanation doesn't seem to be valid:
I tried to actually reproduce the behaviour you are seeing with an 8.7.0 deployment and can't reproduce it.
It looks like your deployment of the apm-package is somehow incorrect / corrupted.
Nonetheless disable_metrics=jvm.fd.*,jvm.memory.non_heap.pool.* still should do the trick for you.