I want to know if I can temporarily access a domain name via the server's IP address for example ip/~username or so
This does not make much sense as it won't work with most modern CMS anyway. If you want to access a site without changing DNS, use this method: https://www.faqforge.com/linux/serv...ess-a-namebased-website-without-a-dns-record/
When is the best time to run 'apt get upgrade'? The safest way to update a server based on ISPCONFIG3 should ensure version compatibility with the upgrade.
You can run it at any time, e.g., daily, as updates installed via apt-get upgrade are always compatible with ISPConfig. Debian and Ubuntu take care not to add any breaking changes in such updates.
My signature has link to unattended upgrades tutorial, which helps set up server so Debian and Ubuntu updates are installed automatically. Plus, I think this is wrong forum for your question and you should have created a new thread since question is not related to topic of this thread. You have been member of this forum for two months, and have written 88 messages. A lot of questions there. I hope you are making a serious effort reading documentation and trying to learn how to use the tools you have before asking on forum?