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.
I’n Windows it is not stored in a keyring but instead in the registry. This has basically the same security threat model as a local key file.
The ssh-agent on Linux will do what you want with effectively the same security. The biggest difference being that it doesn’t run as a system service but instead runs in userspace which can make it easier to dump memory. There are some other agent services out there with additional security options but they don’t change the threat model much.
My memory of the cp command is that attributes such as file times were transferred at the last step. I think this would make rsync safe in most situations where a system crash wasn’t involved.
I think I remember running into that as well but for whatever reason I couldn’t get accelerated-x working with the opengl libraries I was using for school. Likely the issue was just a lack of understanding on my part as I don’t think I had a good grasp of the Linux library loader until well after I graduated.
I’ve had a system in the late 90s with a 3dfx voodoo card. Also had a laptop with a SIS card from the early 2000 era.
The voodoo card was THE card to have it it’s day (mine was an older second hand system though). The SIS card… for some reason they decided that standard VESA mode probing wasn’t a thing they supported and would hardware crash when that API was used. I eventually got it working in Linux after patching xfree86 to not attempt probing when loading the VESA driver.