Edit, after reading your post multiple times, I think I finally got what your problem is.
Maybe it is a Win vs Mac problem because on my Mac I type with my German keyboard just fine on WaniKani. I can either type in hiragana (but I never do because why would I switch if I don’t have to) or just let WaniKani convert what I type and it works fine since in both cases I would use the German layout, type “yu” and it would convert it to ”ゆ”.
Isn’t the problem rather your Japanese keyboard layout on Windows? Shouldn’t it be possible to set it up to work correctly in combination with your German layout? Having to type with a qwerty layout only when typing Japanese sounds… painful. (edit but apparently that is what it is. Unless you want to tweak the registry a bit, that is what I would try if I was in that situation but not sure if that is still possible with more recent versions of Windows)
And since I’m already here I’m going to tell you how I solved the whole thing: I use the Anki mode script. I find it too time consuming to add German synonyms and I often get the English terms wrong because I’m just not a native speaker and I often type an answer that is correct in theory (in my head… ) but just complete nonsense in English. Using the Anki mode is faster, I don’t have to bother with typing errors and I can trust myself to not cheat (too much… ) so I’m really happy about it. Just mentioning it in case you are not aware that this script exists.