I'm rewatching some op arcs. I noticed that BB fruit is very different from logias in that it doesn't turn his body to anything. It's more like paramecia with it's quirks.
We know souls exist (from brooks power), and we also know something resides in DF, otherwise even if you give a zoan to an object, the object would not get 'spirit'/soul to have feelings etc.
If this is the case, we can then assume that for the condition of one fruit at a time to be completed, the tree that makes it (if it appears randomly or not is irrelevant) would need to know that the user is dead, what better mechanism than for the soul/devil to return to it's origin. If we then assume that yami yami can capture those souls (and we already know that humans can live in it's dark space and not die), it is possible that yami yami fruit allows BB to capture the fruits essence and use it. Since he ate a logia that is not actually a part of his body, he would be able to use any one other fruit at a time with his current power, while all other powers reside in him(his dark space, isolated from his body).
This also fits with Chrollo from HxH where he has to keep his book to use a power and can only use one power at a time. It won't become overpowered if the limit is that only one devil/spirit can reside in his body at any time with the yami yami being outside of his body.