I've never had an issue upgrading from a beta build to a "final" build. If worst came to worst, you download a the update off Apple's site and forgo the App Store. If it fails, use Pacifist to force it to install.
You have to see where Apple's tech support is coming from. They are dishing out a canned response to avoid liabilities in the event it didn't work or something didn't go expected. Eg: Some resource or change introduced by the beta continues to linger on even after final update. However, you generally face this risk with any pre-release software.
IMO, the 10.12.1 beta is worth it if you're seeing issues on Sierra and desperately need a fix. The smart move would be to have stayed on El Capitan until 10.12.1 came out. It won't be much longer.