All mentioned in the subj...
I have the archlinux with the KDE installed on it. When I do the log in the kcminit writes the font specified with size of 9pt into the $HOME/.config/Trolltech.conf. I tried this with a new user's home -- no matter.
As workaround I set read-only permissions for the Trolltech.conf.
KDE is 5.9.3.

The code in question seems to be krdb.cpp in plasma-desktop which applies KDE settings to (non-)Qt applications.

Are your font settings themselves correct, though? What does this setting break for you? When you change fonts in System Settings, does it then write the correct values in here?

What do you mean "correct themselves"? I adjust a fonts settings via the KDE's systemsettings. I set the Noto Sans 11pt as the main font in it, but after reload of the KDE the Trolltech.conf always reseted to the Sans Serif 9pt font. And a Qt4 apps use the Sans Serif.

Will be fixed in Plasma 5.11:
https://bugs.kde.org/show_bug.cgi?id=378262