When you say separate VTube Studio instances, do you mean that you have two copies of VTube Studio running with separate sources, or just that the source in OBS is in a different position depending on the scene?
In that case, for now I would recommend applying the same position/scale offset that you've applied to your VTS source to the KBonk browser source for now! Items will appear out of thin air when thrown from certain directions, but the impact should be aligned with the model at least! I generally recommend creating a group for the browser source and VTS source to keep them aligned if you tend to move your VTS source around.
For best results, I do overall recommend keeping both VTS and the KBonk browser source covering the whole OBS screen and using hotkeys in VTS to change the position of your model depending on the scene. That's what I do!
I'll definitely consider some type of calibration profile option to help with this type of situation, but finding a good solution might take some time! Especially one that would be less cumbersome than just using model position hotkeys in VTS. Best case scenario, I'd be able to read scene info from OBS and change calibration profile automatically based off of that!
For now, thanks for using it, and keep an eye out to see if I'm able to figure something out!