OK, I connected the set-top to my receiver with components video and optical audio. It worked, with 5.1 audio (though so far, all the 3D videos from Comcast have only 2 channel audios). So I was able to use my receiver to switch between PS3 and Comcast, without using a hdmi switch. Thanks for the helpful suggestion.
So I have now two ways to watch Comcast. I still keep the original hdmi connection for regular channels, but use the component for 3D programs. The receiver has two hdmi outputs, and I use the 2nd one to connect to the 3D adapter. I added a "3D TV" activity to my Harmony to make all the necessary connections, and it seems to work, sorta. There are still a couple of manual steps that I am trying to automate (or at least reduced to a single Harmony bottun): I need to
1. turn Sammy HL76A750 to 3D mode 1, and
2. select 3D mode in 3dc-100s to either up/down or side-by-side.
Both of these requires pushing buttons to cycle through list of options, and I couldn't find discrete codes to select the exact feature, so it is not wife-proof yet.
All in all, the 3d adapter works as advertised, and I have arrived at a workable setup, so I am happy.
I do wish that Comcast/Motorola can fix the problem with the set-top box. Comcast also needs to document such workarounds in their web site. Their technical support is pretty useless.
Once again, I have found answers in avsforum, in this thread and in others. A big thanks.