I apologize for late answer. I had no much time for reply.
you should be more precise in your description. Which automation list, which host, which platform, etc.
Yes, I use Reaper 5.9 64bit under Windows 7 64 bit. When I click on Track Envelopes / Automation. it show me full list of parametres which can be autmated. Under list I see Bypass, … (other parametres), Bypass.
be sure that the flag Vst::ParameterInfo::kIsBypass is used only for 1 Parameter.
I only use HelloWorld example and there is only one Vst::ParameterInfo::kIsBypass.
Btw. I if I am right, by default VST 3 plugins are two components. Controller and Processor, isn’t a second bypass for Processor? When I automate first, plugin stop process sound, but controller is active, not bypassed. Second bypass turn on/off controller (I can see in reaper window the checkbox checked / unchecked, when is second bypass automated). Am I right?