you are right test which not simulates real life scenarios or does it in very limited way wont be very accurate or it wont make any sense at all. I'm thinking to use flash because in test described in WBM book, how I understood it, author of the book tries to eliminate aperture/shutter speed influence by using stouffer step wedge. So I was thinking if I use flash it wont make a difference for that particular way of testing. Do I assume correctly? What of course is not eliminating problem of exposure variations in taking photos in real life with shutter speeds which are not exactly what we think.
Shutter speed test is a good idea.

How did you compensate for discrepancies in shutter speeds (if you found any) - you adjusted ISO or aperture? Calumet shutter tester - how does it work? Does it display values on lcd or you have to connect it to the computer microphone input and use audio software to read it?