Sam,
Although I agree with most of what you are saying in your last post, short of you still can't design around everything, (whoops I didn't mean to put 120 on the comm circuit or cutting them there wires caused a problem?)

I still don't believe I understand the reasoning behind the explanations given to the OP's statement.
I can understand if you start taking various ground references for your secondary, other than just at the transformer itself. For example at the compressor contactor one adds a connection to the panel base for a ground reference in parallel to the common back to the transformer and then later someone/something causes a disconnect on the common reference at the transformer itself, and now your ground reference at the contactor just became a neutral. Now if we were add to the scenario that the shields are not terminated properly, one end is connected to ground, but the other end touching ground cause it didn't get taped off, and the panel with the compressor contactor (who's common was taken to the panel base) doesn't have a solid ground actually ran to it and so you end up with current a loop, now I can understand a major mess and potential for noise issues. Had a similar scenario years ago with transformers in parallel....
Here's the thing, most controllers I work with allow for a ground referenced secondary so I install them with a ground referenced secondary. While I try to only run shields in areas I suspect may be noisy, I have yet to come across a problem as described in the OP's statement. I've gone back many times and re-pulled shielded wire/terminated the existing shielded wire correctly to fix noise issues. 99.9% of these were in grounded secondary systems, so I can't believe a grounded secondary will cause a problem with a properly installed shielded wire system. I see more shields that really aren't installed correctly, some are close and many are far from it and I see that as the bigger problem.
Also I do agree that systems that want a floating secondary install it as such. Learned the hard way by mixing full-wave and half wave rectified devices and smoked a device/two (that's all I'll admit to anyway

)