This is something that's a little interesting. I mostly just copied the way nachuz originally did it (resulting in what you have now), but that's been done with the assumption that sys-hidplus connects controllers as sideway Joy-cons. When I tried it though, the joy-cons always connect as one half of a pair (both vertical), which I think prevents your controller from behaving as it should.
In short, it's intended and there's no existing setting to fix it, but this was implemented with a wrong assumption on my part. Whether this can be fixed for a later version... I'm not sure. Someone had the same problem earlier and I didn't get around to fixing it, mostly because I don't have a game that uses sideway joy-cons and can't test it as a result. I do have one question (and maybe more down the line): despite the analog stick being sideways, do the controls at least work fine in games that force you to use sideway joy-cons?