LOL - that's why I lead you to that page.
XAMPP (other than the installer) is 100% Windows registry agnostic, that's why the Control Panel is needed, all CLI driven batches.
SO - you can indeed run both, as long as YOU know what they are doing. I have two Apaches and two Perls. I don't run two MySQL instances however, you could do that as well. If its only for testing, you might consider changing the default ports so you can have consistent shortcuts.
A couple thoughts. You could track down the batchfiles used to start the Specific XAMPP services you want, and make them into a shortcut, so you lauch them only when you want to work on Joomla. Even easier, you could also put all the Joomla specific Apache conf directives into a 'httpd-joomla-extras.conf' along with notes on what you disabled in the main httpd.conf (just a thought, as I said)
The thing is all the options and defaults are different (as you know), and at some point, you just wind up scratching your head, LOL.