I understand what you're asking, and you should probably create a default bootup registration so you only have to press a registration button to bring all your settings back to default; unfortunately, you can't save the freeze settings in that registration, as those are global, *outside* of the registration.
Since registration changes are probably what's forcing you to look for the freeze button, you should probably either make individual changes to the registrations that are changing what you don't like (fingering, split point, etc. You can load up the offending registrations, uncheck the portion that you were freezing, and re-save, and they will stop modifying your 'safe' settings. I think you can use Murray Best's YRM (Yamaha registration manager) to remove unwanted registration changes en-masse.
Or, just create your own registrations and that way, they will always only change what you want them to change. I only use my own registrations, no one else's. And I never use freeze because I never have to; each registration changes only what needs changing only, nothing else (for example I only check tempo when I have a registration where the tempo needs to be set or changed; if I tick it on every single memory slot, then if I change it slightly I have to go back and change each one individually!)
Having said all that, the Freeze options *do* stay after you turn off and turn back on; it's not that much work to just press the "Freeze" button every time you turn it on...
Mark