I can confirm that does fix the problem on Fedora Kinoite 43, however PKHeX is then no longer skinned with your KDE theme.
An alternate fix I found is to leave "Allow the window manager to control the windows" enabled, then in winecfg set the "Windows Version" as "Windows 8" on the applications tab.
PKHeX then seems to work fine and is still skinned like any other native app: