I'm not going to comment on the internal Mini54 details. But let's chat about this bit...
The reason it concerns me is that I'm trying to figure out a way to program the Teensy 3.1 over it's serial port. That way I can reconfigure it using an XBee which is a nice-to-have in my application.
Hypothetically speaking, and even before doing so, let me be perfectly clear that this conversation in no way implies I'm ever going to implement such a feature, but nonethless, hypothetically, if Teensy 3.x someday supported a way to reprogram wirelessly by Xbee or other serial communication, how would you propose programming mode be initiated? By this, I mean initiated automatically, without pressing the pushbutton. My assumption is wireless remote reprogramming probably isn't very useful if it can't be wirelessly initiated.
USB auto-reboot works for 2 reasons, neither of which applies to serial communication.
#1: The USB port is automatically initialized and running when your Arduino sketch runs. During the first second or two, the USB host is still "enumerating" the device, but from Teensy's point of view, the USB is always up and running and could receive the reboot request at any time. USB has dedicated pins that aren't ever used for normal I/O. USB also has a fixed baud rate and communication format. Serial lacks all of these features. It doesn't start communicating until you use Serial1.begin(baud). The pins are shared with normal I/O and other important features, so you can't always automatically start Serial without seriously disrupting other potential applications that would use those pins for non-serial stuff. Serial also lacks consistent data rate, data format, so you don't even know in advance what baud rate is needed.
#2: USB has a well defined data format that supports multiplexing many virtual data streams (called endpoints), and also has a message delivery mechanism (endpoint zero) which runs simultaneously. Control messages can be sent to request a reboot, without disrupting the other streams, as seen by the application code running on Teensy and also on the PC or Mac that's communicating with Teensy. Serial lacks all of this. It's just a single stream of bytes.
Arduino uses one of the serial handshake pins to cause entry to bootloader mode. Were you imagining connecting an extra wire, solely for the purpose of initiating programming mode?
My concern is that if I mess up after a full chip erase the USB portion of your bootloader will be missing and therefore my Teensy will be bricked. Is that the case?
If you go messing with this stuff in unsupported ways, you may indeed brick your Teensy. I don't want to discourage you from hacking and experimenting, but you really do need to accept responsibility for damage if you go down this path. My advise is this:
buy spares!
If you do try this stuff, another good idea would be carefully saving a copy of the code and steps you're using on each attempt. If you do end up bricking a Teensy, at the very least keeping good notes can help you avoid making the same mistake again on your spares. It's also give you something you could send to me, which won't necessarily do any good, but the odds of a positive response from me are far better than a poorly described "something went wrong" report.