1) no, because the end result for both of them is the exact same. You'll end up with the same configuration (B9S + LumaCFW) no matter which you follow.
2) when you do ntrboot you use a DS flashcart, and at the end you can reflash it back and use it to play DS games. With frogminer you don't use a flashcart, but you can use
TWiLightMenu++ to play DS games even without one (not all games are compatible, but most ones are). Or, if you already own a DS flashcart, you can use that for DS games
3) if you're doing ntrboot, you don't need to worry about FW version. If you're doing frogminer, you need to be on the latest firmware (11.9), but if you're on an earlier firmware you can just do a system update and proceed
4) technically yes, but there's almost no reason to uninstall CFW once you have it. Again, the end result doesn't differ between the methods, so there's no reason to reinstall CFW once you've already done it with frogminer
5) the R4i Gold 3DS Plus is the best DS mode flashcart that also works with ntrboot