Sorry for the late response here but I knew that I was going to need some time to explain what I know and discuss solutions. There’s a long story to how we ended up with the current ShadingControl situation and the changes that are taking effect have required coordination between the EnergyPlus contributors, the IDFEdditor maintainers, the OpenStudio team, and us. Because of all the people involved in this change, this sequence is still playing itself out and so there are going to be some incomplete and unsatisfying situations for a while.
I know that much of the underlying reason for why people wanted this change is to allow better coordination between the blind-pulling/electrochromic behavior in daylight and energy models. Part of this involved moving the specification of ShadingControl object on the FenestrationSurface objects to the other way around (specifying the FenestrationSurfaces on the ShadingControl). This way, more complex sequences of blind-pulling across different windows could be modeled with one shading control object. However, this creates a non-backwards-compatible change, which is probably why they decided to make the change around the shift from E+ 8 to E+ 9.
Honeybee (trying to straddle both old and new versions of EnergyPlus) is still kinda set up to use the old way, which results in many FenestrationSurfaces being set to one ShadingControl and the situation you experience here. Realistically, this is the only way that we can ensure Honeybee is still fully compatible with OpenStudio 2.5 (the version where we know that everything is stable) but still work with the new EnergyPlus /OpenStudio. So I think that we are probably going to leave honeybee-legacy as it is for now and, if you really need to avoid the painful situation you describe with honeybee legacy, our answer is just to use OpenStudio 2.5 and you will not experience it.
However, now that we have the opportunity to fully revise Honeybee (the new honeybee-energy library is nearly at an MVP level now that it can produce simulate-able energy models), I think we will set up ShadingControl with more of a “new E+” philosophy. Namely, I think we will just write out individual ShadingControl objects for each and every FenestrationSurface. This is clearly going to increase the size of the resulting IDF file but it means that you will never experience this headache that you currently have. While it’s still going to be lacking some of the HVAC capabilities, ShadingControl is something I think we could put in the release of Honeybee[+] that is currently planned for Spring 2020.
Let me know if this set of solutions sounds like it will work for what you need or if you have an alternative suggestion.