I am in no way an expert, but I don't think alot of what you ask for is possible. As stated many times, there is no inherent way to lock the orientation of someone else's app (and for good reason). I'm guessing what the dev's are doing is a hack (hence the menu item). Once an app is opened you can set the acceptable orientation of the Storm. I assume all there menu item is doing is calling the code to lock the device to a specific orientation. You will have to ask them to be sure. While it is probably likely they can develop a way to persist the settings across reboots, I see two particular landfalls (possibly three for the devs).
1) The device locks the orientation at startup. Most apps that lock the orientation do so before the screen is displayed so it is forced to a particular view. Once the app is started this cannot be done. So if you open the phone in portrait and have it set to lock in landscape it will lock a portrait layout in a landscape view (ie one side of the screen will be blank).
2) Everytime they add the ability to lock another app, you would have to redo the settings for all of your apps, unless they save the data to your phone and and not the OS memory space. This would slow down the app greatly, as they would have to read a text file on every device startup and lock all of the apps, or do this on every app that opens.
3) For them to do this for all 3rd party apps, they would need to either get the name of the internal file (as named by the dev) or buy every 3rd party app so they can look them up.
Like I said, I'm no expert, from what I have read on BB development, those are the likely issues they are running into. As well, they should be applauded for having the ingenuity to think of the idea to push global menu items that allow you to even lock other apps.