GNOME Boxes lead developer Felipe Borges has been overhauling the application with a major rewrite and today announced the new beta release. GNOME Boxes has migrated to using the GTK4 toolkit and libadwaita. The new GNOME Boxes code can also handle installing Microsoft Windows 11 now without needing any manual workarounds for Secure Boot or TPM requirements.
The new GNOME Boxes code also introduces a VSOCK device for accessing VM contexts and other improvements. With the revamped GNOME Boxes, it's also shifting to a Flatpak-first and only model for distributing of new GNOME Boxes releases.
You can't prevent people from using older versions. New versions need to be tested, by the time this process is finished, upstream already released a newer version.
If you use the talking point of "own customizations", did you get that from the mint thread and did you read it through? Software should come as is, but in some cases devs work slower or have other priorities so I understand bugs get fixed some other way. The whole pipeline from dev to user isn't as simple as you think.