Interesting stuff. It just goes to show that there is truly no perfect solution. Your idea of using two different controllers to have different IDs is actually very smart, props for that. I'm also thinking that would nullify my problem I had with Xpadder before with multiple controllers when using RUI's built in keymapping.
For a long time, I used Xpadder's standalone keymapping, as I found it a fairly stable solution. I learned all the quirks and worked around them, until I eventually reached the 255 profile limit, that I didn't know existed. I was pissed. I felt like all that work was down the toilet, then I moved on to JoytoKey.
RocketLauncher's Keymapping would be perfect, if not for a few issues that for me are deal breakers. The biggest issue is that it causes loss of focus in Launchbox (but not HyperSpin). All that needs to happen to make it work is a single mouse click to make BigBox active again, and there's even a setting in RLUI that's supposed to do that, and when you troubleshoot with a log it will even tell you that it does that, but, it still doesn't work.