I'm not sure exactly what you're after, but the Hiragana Pro/Katakana Pro apps (android only, I believe) have two practice modes: choice from three pronunciations as you mentioned, as well as typing romaji with no hints. The latter makes it abundantly clear which kana I'm shaky on.

They're also each a dollar to unlock voiced/combined readings and remove ads. My pihole did block the ads while I was just trying them out.