There is a difference between mandating that your customers use one specific Linux distro which is maintained by a controversial company, and supporting all Linux distros through an imperfect-but-fully-working method.

Sure, you'll still get a few complaints from ideological purists, but there's no avoiding that regardless of what you do.

Can confirm, I hate flatpak

This feels analogous to the old Google latency improvement story - improve performance and p99 goes up, not down, because more people are now able to use your product.

These angry customers are a symptom of having more customers; in this direction (compatibility) companies shouldn't be KPI'ing on angry customers.

It is very legitimate that high compatibility means more very obscure, low value, high cost, bug reports that are hard to classify as such. And my gosh, I hate working with rude ticket writers.