Since vocab terms with alternate kanji have been put together in the same entries in the dictionary, perhaps the same could be done for terms that can be written in both hiragana and katakana and have entries for both. Terms like plant and animal names, onomatopoeia, etc. It would make the dictionary more consistent, and perhaps allow certain terms that also have kanji to share the same entry even though they don't currently (despite the above mentioned merging, there are still 3 separate entries for terms like バラ and ヒマワリ, presumably only because they are not all written in the same kana system).
The condition for the merging currently in the system is nothing other than "are they marked together in the original edict dictionary database". What you are proposing could be done, but it would have to be done based on the contents of the entries. They would need to share the exact same dictionary, and as you said, same kana base. I am about to (tomorrow, most likely) put up the August beta, and while there is still a lot of work to be done there (and I'm extremely excited about that), I might be able to try throwing this in at some point.
