We checked the multiple GPU theory with an external GPU (eGPU) and we can reproduce there as well. This definitely puts the issue in Apple's court so we're going to open a bug on bugreporter. We'd suggest you to open a bug with Apple too, on bugreporter or on the normal support channel if you are not a developer.
In terms of workarounds this is very tricky indeed. Let's see if we can come up with something that does not cause issues elsewhere.
Carlo
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