OC please steal
- I believe there is still an issue with Windows deleting Linux bootloaders during some updates. You'll be fine if you install Linux on a separate disk, and even if you dual-boot on one disk and the bootloader gets deleted, there are ways to recover it. You don't strictly need to have separate data and OS partitions, and I've gone back and forth on whether I prefer it - it makes distro hopping and disk encryption easier, at the cost of potentially inefficient use of space and serious consequences if your OS partition fills up.
- Disk encryption is very straightforward if you use separate OS and data partitions. You literally just tick a box during the install and enter an extra password. It won't upset Windows any more than a normal install does (i.e. Windows might think it's corrupted, but won't do anything without your input). With one partition for everything, it's still possible, but the encryption will be much weaker and handled by the bootloader in a somewhat clunkier way, and I'm not sure if Mint even supports that setup.
- I don't have much experience with this myself, and certainly not on Linux Mint, so I'll leave this one to other commenters.
- Synaptic is just a fancy frontend to APT, and I think Mint also has something called mintInstall, which was just an apt frontend back when I used it, but I think it also supports Flatpak now. It's entirely up to personal preference as to which UI you prefer. I do recommend you set up Flathub if it's not there by default, as it gives you access to a ton of useful apps that can't be packaged by Debian, Ubuntu, and Mint for various reasons.
- Don't download software from random websites unless it's absolutely necessary. Chances are, their version either won't work well, if at all, or will break your system. Try APT first, Flatpak second, everything else is a last resort option. If a program you used on Windows doesn't have a (working, native) Linux version, try finding and learning to use an alternative that is in the APT repositories before downloading the Windows version and using it on Wine. Back up your most important files from Windows before installing Linux in dual boot, just in case you make a mistake somewhere. To answer the last question, stick to the default terminal emulator and Firefox installation unless there's a feature you really want in another one; the distro's developers picked them for a reason, after all.
Going by their Mastodon account, seems they were erroneously detected as "from a US-sanctioned region" and it took too long for said error to be resolved, so they just made the switch.