Figured I'd give a final followup in case anyone else has these problems. In general, I can't recommend using Gentoo for this.
It looks like it did create a crontab, but because the asterisk home dir is not in the usual spot, the permissions were wonky. Once I fixed that, had no problems Applying Settings.
Beyond that the asterisk compile that Gentoo creates doesn't seem to support pjsip properly. FreePBX exposed it, let me set up extensions as pjsip, but try as I might asterisk itself never showed any ports open for it (as per netstat) nor showed any response to login. Old chan_sip did work... but for whatever reason I couldn't get ICE support to work for google voice as I kept getting the "Unable to add Google ICE candidates as ICE support not available or no candidates available" no matter the options I set anywhere.
Once I compiled my own version of asterisk, with pjproject and pjsip set up and ICE properly selected, everything Just Worked. So I'm good to go now, but Gentoo definitely has some extra steps involved that sort of defeat the purpose of Gentoo by having to manually compile several things. Thank you for the fixed version though; that did at least get FreePBX going!