My purpose was to keep the cost and complexity of devices down by eliminating the need for their own power supply (or even batteries) for the ones that take a small enough amount of power that the controller would hardly notice the load. This eliminates the need for some of the wall-wart power supplies and their cords, mess, and expense. BTW, I've never seen a modern requirement for -5V. That seems to be something older than 7400 TTL and the 6502, so I won't ask for that. If someone needs it, a 7905 or 79L05 is small and cheap way to get -5V from another negative voltage in the range of -7V to -30V. OTOH, you could also use an LT1054 switched-capacitor voltage inverter in an 8-pin DIP to get a regulated -5V from an input of anywhere from +6 to +15V, using four capacitors and two resistors. I have one breadboarded here and got a 0.06V drop at 87mA, meaning a 0.67-ohm output while it was able to regulate! The regulation is essentially analog though IIRC.
I don't expect any problem as long as the bypass capacitor leads are kept short. I can't claim to have this exact type of experience but I did work in VHF & UHF power transistor applications engineering in the mid 1980's, and it's also similar to the matters of keeping stray noises out of our audio systems in aircraft installations. We had to be very specific in the installation instructions because otherwise technicians tend to think ground is ground is ground, and they think they can connect any and all grounds to the airframe just because there's continuity between them already. Then they get all kinds of noises into the system.
I addressed this on my workbench computer's data converters where I don't even have a ground plane, let alone one with a chainsaw line. DC-wise, you'll find continuity between digital grounds and the audio jacks' grounds; but they're not the same AC-wise, and the digital noise does not get into the analog signals or disturb the converters. I also addressed it in our aircraft audio system designs where I had switching power supplies on the same boards with audio circuitry where the switching noise had to be kept out of the audio. It can be done, although a novice probably won't get it right, which is a consideration.
Without the negative-voltage power, certain things won't work right, but I can't think of any damage that would be done. The cheap RS-232 line drivers that don't produce their own negative voltage just won't be able to go below ground for valid marking, the outputs of the higher-performance op amps that want plus and minus power supplies won't be able to get all the way down to ground (meaning they'll distort), LCDs requiring a negative backplane voltage (common for STN) might appear blank, some D/A converters won't work right, etc.. There's a small risk of damage if the device expects to be able to get positive supply voltage from the bus and there is none when positive signal voltages start arriving.
If the controller puts power on those pins and the device has the bypass capacitors, no problem. If the device shorts the line to ground and the controller tries to power that line, the controller should have some sort of protection. On the rare occasion that I turn the power on to my workbench computer and have something shorted, right away I see either the excessive current or the fact that the power supply's output voltage dipped because the current limit kicked in, and I shut it down. You're right though— this thing needs to be a little more foolproof is we expect it to be used by a wider range of users.
What I might have to do is add a separate power connector, like disc drives have. I just thought it would be a cleaner setup to have it all in one connector.
Would you ever need two or more things to be able to act as a controller in the same session, or can you (the user) tell one to be a device for a particular session? The two hand-held computers seen at http://www.6502.org/users/garth/projects.php?project=4 are both equipped with HPIL (Hewlett-Packard Interface Loop), and I have used them to control and take data from a lot of equipment. (Especially in the 1980's, people would freak out to see a hand-held device controlling a stack of lab equipment in a rack!) The larger of these two hand-helds does not insist on being the controller, but the simpler, smaller one does; so the few times I've connected them together to transfer data, the smaller one was the controller.