So to pull these ideas together, aiming for a single box, with the option for some added weight (concrete is an option, but sounds a faff to prepare and somewhat messy; but lead shot / scuba diving ballast is still readily available and could be poured into a 3D printed cavity and sealed in), and some damping/isolation for the microscope, with the electronics box (with its vibrating fan) maybe off to one side (or in front, to keep things elegantly symmetrical).
Keep using the ribbon cable for the camera rather than anything more substantial like an HDMI cable to reduce vibration transmission - assuming we are still okay with the ribbon cable length.
I note on my 3D printer there’s an option for it to have anti-vibration feet, which I think are just TPU, so I wonder whether some form of coupling made of something like that would work to isolate the microscope from the box stand below it - either as a purchased part, or even 3D printed. I think the world of top-end hifi systems put a lot of thought into vibration isolation, so there may be some concepts we could borrow from there.
I also hanker after having the option of an integrated small touchscreen, which one could envisage sat on top of the electronics box part, in front of the microscope, tilted towards the user.
I could try modelling something if that would help, but it would be in Onshape rather than OpenSCAD.