Yes, maybe to set up different Pleco "environments", with different Flashcards databases (or just the ability to pick a specific flashcard database for a particular environment--it can also be the same database), different dictionary search order and different Dictionary Search Histories, and perhaps even different general settings for each environment may be a cool thing to have. Then users who do not like a precise distinction could go on with one Enviroment, while others, like me, will appreciate the clean separation between environments, to have in one place what belongs together.
I think your last suggestion of having multiple card definitions seems harder to master, because then the user would probably have to set up which flashcards categories allow different definitions and which categories don't. But having different Pleco "Identities" would be like having more than one Pleco--a very familiar concept that also exists with multiple user accounts on Mac OS X/Windows, for example. The File Manager file hierarchy could still be shared amongst different Identities.