Just want to add something to what I already wrote.
Do not try to accommodate all use cases! There is no software package (apart from several of the "free software" ones) that do this or should do this. Trying to make software that works for everybody might result in software that works for noone. So, I would, for example, totally exclude the use case of live performance. A complex soft synth is not a live tool.
Also, I would suggest sticking with one decision and not adding huge amount of options "for all those other use cases". This is the problem of many free software projects. If you decide to go for single window, stick with single. If you go for multi window, stick with it as well.
And again, apart from asking opinions of this, I must say, very small community, reach out to people who use other synths, talk to people at KVR, for example. Make sure that if you go multi-window, for instance, this is a well thought out decision and not a "free software tradition" (not saying that multi-window is not an option, although I personally know of no well established synth that has multiple windows).
By the way, a case that you might also consider - are you thinking of Zyn only in terms of standalone software or also a plugin inside a DAW? If it is inside a DAW - is it a good idea to have multiple windows? How will the synth look in side a DAW?