It can still have issues with potential attacks that would redirect your client to a system outside of the VPN. It would prevent MitM but not complete replacement.

Likely you needed to include the intermediate cert chain. Let’s encrypt sets that up automatically so it’s quite a bit easier to get right.

There is also SMS passive reading using LEO intercept. Hacked police email accounts are used to gain access to carrier systems where they use “imminent threat” no warrant lookups to pull the SMS in real time.

SMS is a terrible form of 2FA, better than none but not by much.

Your experience may depend on which distro you use and how you install things. If you use a distro with a stable upgrade path such as Debian and stick to system packages there should be almost no issues with upgrades. If you use external installers or install from source you may experience issues depending on how the installer works.

For anything complex these days I’d recommend going with containers that way the application and the OS can be upgraded independently. It also makes producing a working copy of your production system for testing a trivial task.

Are they on a local disk? Thunar doesn’t render any thumbnails for remote storage by default.