The concern lies more in FFlags that do stuff with data that is saved to the site.
I recall one time when Roblox was working on Color3 support for Parts. I had enabled the flag and saved changes to my place, and then the color data got corrupted. It is especially dangerous with stuff like DataStores.
Ultimately the point is this: Roblox has FFlags in place to guard against potentially faulty code. If you circumvent those protections, we cannot be held liable to any data loss or errors that you might run into. That doesn’t mean you are 100% guarenteed going to lose data if you enable something early, but just exercise caution if you don’t know what something actually does.