Sorry that I've created some confusion for you. Let me tell you what happened to me, then you can decide what to do:
I put the tweak Overboard onto the dock of my SBSettings app. It uses/hooks into Mobile Substrate (MS for short). It seriously messed up my SBSettings dock, in that I could not remove it from the dock and I never could put anything else on the dock. The only thing that fixed it was the upgrade from iOS 4.2.1 to iOS 4.3.3 - it was that messed up. I made the decision then to never put anything into the SBSettings dock that tied into MS. So, that's me and my story. I can't say this would happen to anyone else - so my apologies for throwing that bit into my comments on SBSettings. It added confusion, for which I am sorry/regretful.
You can tell which items that hook with MS by opening SBSettings and selecting "More." Then, scroll down until you see the line "Mobile Substrate Addons." You'll be provided with a list of tweaks that are "on" with MS. Note that you really don't want to mess with them, especially if you're, like me, a non-programmer/tweaker at the OS level...
To repeat, what happened to me may not happen to you. I was just passing on an experience (and my conclusions from it).
AFAIK, it doesn't matter with App Store (read: stock) apps. You can put them on the SBSettings dock all day long and they'll work fine. It was just that one tweak, for me, from Cydia.
I hope this clears things up a bit. Again, sorry for the confusion and the FUDing about using the SBSettings dock. Let me know if that helps.
Marilyn