Do the 'OS X Beta Seed Program' updates wipe your existing OS install? I've joined the OS X Beta Seed Program but am not sure about this detail. Does it upgrade 'in place' and all your countless system tweaks and customizations are kept in tact, or does it do a 'fresh' install and so you are forced to restore from backup all your apps, tweaked system files (such as defaults write variables), third-party prefpanes, and maybe even user documents, at your own initiative?

I didn't see anywhere that they address this.
"Upgrade in place" doesn't touch your data, in theory. However, I would always backup your data before installing, especially beta releases. It's not supposed to change your data, but that's not guaranteed, particularly in a beta release