How do folks handle datasets where different cell populations have wildly different mitochondrial percentages

[JasperGattiker]

I'm working with stomach samples, and the rule-of-thumb 10% mitochondrial percentage cutoff eliminates nearly all active parietal cells. Extending the cutoff to 60% captures my parietal cells, but probably also captures low quality cells from populations with lower energy needs. When you work with samples in which the quality control metrics that capture intact cells vary between populations, how do you handle that?
At this point I'm considering scaling everything right off the bat, splitting the object based on expression of a marker gene, and doing separate QC on the 2 objects before merging them again.