RE: cert warnings - Fair point regarding config changes being a reasonable solution. However, there will be many people that:
- Do want to enable and use HTTPS via using the self-signed cert
- Do want to change the default pihole FQDN from pi.hole
- Don't care if the self-generated cert matches the new FQDN or not, as enabling HTTPS is the sole objective.
In this respect, people would then have the same 'accept SSL/TLS exception' web browser workflow to access pihole as with other locally hosted web-services with similar self-signed certs e.g. Cockpit etc. Sure, they could setup a reverse proxy, or use ACME certbot and a legit domain they actually own, but most probably won't bother. That should still be ok for pihole, and not generate a "CERTIFICATE_DOMAIN_MISMATCH" error on every single restart of piholedns. If you want a practical means to enable an exception - surely a toggle option to "ignore certificate domain mismatch errors" under Settings -> Web interface/API that is exposed only in 'expert' mode would provide an easy way to do this. Those that want it, can find it. Those that ask for it can be readily directed to it e.g. in an FAQ or other docs. An option to re-generate the self-signed cert for the user-defined FQDN would also be a valid solution.
RE: Cronjobs having the potential to silently break things - agreed and understood. I get that. It shouldn't be required, but there is also no harm in giving beta testers, who are signing up for things potentially breaking, a pre-defined cronjob and the option (if only during beta - perhaps via the 'reconfiguration' workflow, or via another web-settings tick-box) to enable it without creating a cronjob manually. If you recommend daily updates, make it easy to do.
This could help keep a majority of people on a smaller and more consistent range of dev builds. That would both reduce the bug-report overhead for any breaking issues that are quickly fixed, and also help ensure the bugs reports you do get are less likely to be for stale builds.
The point about silently breaking things via cronjob is entirely valid, but this is beta, and shouldn't be in prod as breaking changes are to be expected. The v6 beta disclaimer on shifting branch already makes people sign-up to that.
As many people will run more than one instance of pihole either physically or via docker, even if run in prod, so long as there is a non v6-instance as secondary DNS people still shouldn't care if the beta build breaks. As again, they quite literally signed up for that 
If you're concerned about visibility or tracability of cronjob issues, either flagging when the job will run when the option is enabled, and/or redirecting the job command output to logs would be easy wins. You could equally set a flag that is user-discoverable via 'pihole status' should the update cronjob command return a non-zero exit etc.