On the topic of potential crossover elements between the DMD and Melody (and maybe future MrDots games), their Lead Writer had this to offer in Discord:
I took this to mean that, despite original intentions to use some crossover elements as "funny" and unrelated cameos (e.g., the older female nudist), the presence of Koko kind of blurs the lines there. But, they haven't really talked about what this could mean between these and/or future games - or, whether other characters from Melody or DMD might have meaningful or throwaway appearances in their future game(s).
Therefore, what started as a lark could actually mean something more. Even HearzAM admits that the Koko interactions between the current games could reasonably imply a timeline difference between them: while that could simply represent to separate universes with identical Kokos, I think the more reasonable idea is that the nature of her multi-game appearances furthers the possibility that they could exist in the same universe, just different places and times.
I feel that growing these connections could add a rich undercurrent of unsaid subplots to the main stories, where secondary characters or even minor events in the lives of main characters might indicate more happenings in the larger MrDots universe that we are still growing to appreciate. At least, that's what I'd enjoy considering, given how their style is very much about building a story from the ground up: these subtle connections could offer much stuff to chew on without their needing to overtly develop full storylines in their support; our imaginations could do the rest from little clues given.