I have this same issue. Mostly my post repeats/confirms things others have already observed, with a few added details.
Certainly this is a bug in the software. I have filed a bug report with Apple, but heard nothing back.
It seems that the Magic Trackpad driver conflicts with the built in trackpad driver in some ways. For example, I can only see one of two possible "trackpad" panes in system preferences at a time. There is one installed by the magic trackpad that has options like the three finger drag gesture, and the built-in one that has the option "ignore accidental trackpad input", which I can now only see when the magic trackpad is disconnected.
I think my OS now believes that the built-in trackpad
is a bluetooth device, and thus won't shut off bluetooth unless I have some other pointer installed (like a usb mouse). Indeed, installing a USB mouse allows me to turn bluetooth off, and then the built-in trackpad still works fine, but I have to plug in the USB mouse again every time I want to turn off bluetooth. This occurs even when the machine "knows" that there are no bluetooth devices connected (and when the magic trackpad is bound to another machine, left at home, removed from the devices list, has no batteries, etc, etc. Clearly the issue is in the driver software, not the bluetooth link itself).
Having the magic trackpad drivers also seems to greatly increase the sensitivity of the built-in trackpad. For years I have never had any spurious trackpad clicks from this MacBook, but since installing the magic trackpad drivers, I get them all the time.
A friend of mine who has a very recent MBP doesn't have these issues. We are guessing it is because his built-in trackpad is already "magic". He also didn't need to intall the driver update to get full function out of the magic trackpad.
Seems like this add-on driver is really buggy. I'm a little annoyed that Apple hasn't responded to my bug report, and encourage all of you to file your own reports. (I also got extra annoying-sauce with y update, since I learned about the "bluetooth can't be disabled" issue at the beginning of a 5 hour plane flight, on which I had been planning to use my Mac.)