The problem is not applications doing it wrong, and the Gnome
appearance configuration doing it right, they all change things at the
wrong level which explains why the changes are not shared, conflict,
and are a PITA for users.
The right desktop level for DPI is xorg. All the apps need to be fixed
to stop meddling with DPI values, use the Xorg DPI values directly
(and fix xorg when it's getting it wrong, in your case vmware side).
Unfortunately so far the reflex of every app writer was not to help
xorg fix its code but workaround it locally in various conflicting and
incompatible ways. What you are seing right now is the pile of dpi
workarounds and bandaids crumbling on your system.