I’m just linking my own post here for clarity.
Basically, when you launch SG desktop it bootstraps (loads) into a Site config which is this one:
When you then select a Project it will load into the project config which could be your own altered tk-config-default2 or something else.
The desktopserver runs at startup of the Desktop app so it runs from the site config.
If you want to control the versioning of the frameworks like tk-desktopserver when Sg desktop boots up you need to fork the GitHub - shotgunsoftware/tk-config-basic: The configuration driving the Flow Production Tracking Integrations. and change it to your liking, then upload this to a new Pipeline Configuration on your site that has no Project link.
This then effectively overrides the site config.
When playing around with this please make sure to restrict the site config to yourself so you don’t inadvertedly break everyone else’s ShotGrid Desktop loading.
Once you’re ready you can unrestrict it ready to force it onto everyone.