All CFW are basically files on your SD card. There's no reason where drag and dropping would not work.
The only thing that burns fuses is the stock bootloader of the Switch. It burns fuses when it detects you are running a firmware higher than the fuse count. This can get triggered when you normally turn on the console without RCM, install a system update downloaded from online, or install the exFAT patch downloaded from online.
What do you mean "powered up as normal"? Does Album load the Album or the Homebrew Menu?
Checkpoint is just a save manager while EdiZon is a save manager
and editor. And there's no reason to not trim any .XCI files. Lastly, unless you plan on injecting those certificates into header-less .XCI files to play them online, you don't need to dump them. If you do inject them, be aware Nintendo can detect if the certificate doesn't match the base game which may result in a ban.
No homebrew that does it but there is this
website you can check out.