Also need a way to choose which scene to put the objects in.
There doesn't appear to be a way to clear the renderer manually. Also, when rendering a scene, it appears to clear it as well, which makes it impossible to render two scenes?..
What do you mean clear the renderer manually? What do you need that for.
You choose the scene with the "pick scene" action in Q3DMaster. Then any action created objects are in the new scene. Also if you use "change parent to scene" objects will be put in the new scene, so you can code a simple function to move objects over. I didn't and won't include a scene chooser within the various plugin properties in editor for the main reason that the feature is only really intended for limited uses where multiple view-ports are needed, and is difficult to work with due to the abstraction, also there would be no easy way to initialize a new scene nicely in editor. It's not a lot of work to make a function that moves necessary objects over at layout start if you put all the models / etc in a family.
I don't fully understand what you want out of the renderer. Rendering doesn't clear the scenes (you must mean something else, that has to do with the clearing of buffers) also, I have no idea what you mean by clearing the renderer manually. Are you referring to the various settings three.js gives control over when rendering? Q3D doesn't allow access to those levels, but you can layer multiple renders by layering Q3D viewports.
As for the transparency, In general transparency in forward rendering is a difficult issue, and you might simply be running into depth sorting problems with no easy fix due to the design of forward renderer. In general you can use the the "depth settings" on the material of objects to control how they modify/read the depth buffer in rendering.
I'll look into the issues you've brought up when I have the time.