Honestly, I believe that, except for Russians or anyone whose language isn’t derived from Latin, using a US keyboard for programming is best, because you won’t be missing many keys. Maybe the French will miss the ç, but you can learn the Unicode just like I did with the em dash and quotation marks:

• Em Dash (—): U+2014
• En Dash (–): U+2013

Quotation marks:

• Left double quote (“): U+201C
• Right double quote (”): U+201D
• Left single quote (‘): U+2018
• Right single quote (’): U+2019

“tools to use” Timone and Pumbaa taught me to type. https://www.reddit.com/r/lionking/comments/r4wykl/help_how_to_install_and_play_disneys_adventures/

Mavis Beacon is another popular one. https://en.wikipedia.org/wiki/Mavis_Beacon_Teaches_Typing

I bought Typing of the Dead to practice new keyboards when I get them. https://en.wikipedia.org/wiki/The_Typing_of_the_Dead

I use keybr. Another good one to get your speed up after you’ve learnt to touch type is monkeytype

I’ve heard klavaro is pretty well liked with regards to typing https://klavaro.sourceforge.io/en/index.html

For Q2: I would recommend your native layout. I’ve not tried US QWERTY but I tried DVORAK many moons ago because it’s “better”, but I found it’s better to be good at one layout than to try split your efforts. If you’re not doing something where speed is crucial, just use what you’re used to. If your keyboard layout is not good for your purposes (e.g. typing a character you need often for the programming language you’re using, is difficult on your layout), you could remap individual characters or maybe there’s a layout similar to your native one but better for programming. But no need to use US QWERTY specifically. Also as another commenter said, typing speed isn’t that crucial for programming. I find I’m always limited by thinking speed, not typing speed.

1. Can’t help you there as I learned on a manual typewriter years before I saw a computer.
2. Editing on Vim/Neovim is really only good on US qwerty layout. It doesn’t matter too much on Emacs unless the layout you chose is missing the symbols for your programming language or you’re using evil mode. I had a hard time on a Latin American layout and switched to a “US international, no dead keys” layout. I can type in Spanish quite easily with this layout, it is Right-Alt pressed with e to get é for example. And I use the same layout for programming. The Latam layout I typed 'e to get é but the dead key single quote meant I had to type quote followed by a space to get a quote while programming. I had to change the physical keyboard to a US layout one to get everything right. Without doing that [ and ctrl-[ were on different keys, for example. It took some searching in the shops to find one but it was very much worth it.

What tool or program would you recommend for learning touch typing on Linux?

I don’t have a particular recommendation, but in addition to local applications, there are also websites that you can try. The keyword you want to search for is “typing tutor”, e.g. on Debian.

For someone whose native language isn’t English, would you recommend learning on their native keyboard layout or switching to the US QWERTY layout for programming purposes?

For programming, the most important thing is that you can type the full set of characters present on US-QWERTY without too much acrobatics, because programming languages tend to use all/most of them.

Other than that it’s just down to your preference and comfort. I don’t recommend putting stock on any hype related to typing speed.