I'm sure you're not missing anything! I'm just confused - and probably also being confusing.
I'm using a variant of sv-dvorak so, for example, my left hand home row is AOEU instead of ASDF. As I understand it, what happens at the moment is that the keyboard sends, respectively, the scan codes that normally map onto ASDF but the operating system maps them onto AOEU instead (unless in recovery mode, which I admit is rare). The bottom left key, say, undergoes a slightly different remapping because I use xmodmap to change it to the Ä character, whereas the O/S keymap thinks it's a backslash.
My concern was that I would end up with the O/S remapping scan codes to something else, but I have probably just misunderstood the whole thing (haven't done this before). I take it from what you say that if I hit that bottom left key the keyboard will send the scan code for Ä and it will look to the O/S as if I had hit the key that character is normally on. Does that in fact mean that I should use Swedish as the language? I currently use UK English, dorakukp variant, with xmodmap adding the Swedish characters as well as moving some of the other keys around. I don't know if either the UK or US character sets contain the Å, Ä and Ö characters. Or doesn't that matter? Sorry, I'm a bit muddled about all this!