Thanks Hasu! Your answers confirm what I feared... Oh well. So much for using the caps key as the LGUI. I think at some point, I will consider replacing the internal controller for something else and do away with the ADB converter. Before I do that, I need to tear down the keyboard and map out the matrix. If I can regain differentiation between the L/R command key without too much hacking of the PCB, then it might be worth it.
Right now, I am using space-fn since the command and caps behavior limit the keys I have to choose from. That seems to be working ok, but I feel that there are times when it doesn't quite register correctly. Not sure if that's a converter or a keyboard issue.
BTW, your TMK firmware is amazing. I now have it running on two keyboards (Model M with phosphor glow controllers and now this Apple keyboard as an ADB converter).