It would be nice if such a feature were implemented, I agree.
In the meantime, there is a pretty good workaround which I would highly recommend, which is to liberally use the User Synonyms / Manage Synonyms feature to supply yourself with extra synonyms to ‘disambiguate’ different kanji and – even more so! – different vocabulary.
For example, I personally have manually added the user-synonym ‘Cause’ to 由, and ‘Logic’ to 理.
As I’ve progressed in levels, I’ve been using User Synonyms more and more to help conceptually distinguish between different items that are frustratingly similar.
Often, the ‘synonym’ is not even meant to be used (by me) as an actual ‘answer’ during a review session. Instead, it’s just a bit of extra info (like a ‘tag’) that I can quickly scan from the item’s info, for example if I get it wrong.
For example, 用意 means ‘Preparation’, but there are a ton of other vocab that also mean ‘Preparation’, so after looking it up on Jisho.org, I found that 用意 also means “preparation; arrangements; provision; getting ready; laying out (e.g. a meal)”. And so, since ‘laying out’ is unique to this vocab, I decided to add ‘Laying Out’ as a user synonym. However, since ‘Laying Out’ on its own doesn’t seem (to me, personally) to match with ‘Preparation’, I decided to include the example (of a meal) into this user synonym.
Thus, the actual user synonym I use is ‘Laying Out (a Meal)’. Now, I don’t actually ever intend to type out the whole
laying out (a meal) during a review session. Especially with the parentheses! I’ll just type
preparation instead. But for the purposes of disambiguation, having a longer ‘synonym’ that at least makes it clear which ‘Preparation’ this one represents, is all I really care about. It’s a workaround, after all, not a true solution.