First, don't put any good little 12V+ source there, as it will connect to the PWR fuse in normal operation. so you need to tap THAT fuse. You don't want to bridge two fuses.
Second, as to the diode question, the honest answer is I don't think so. The issue is the modules, such as the Body ECU, are not detailed as to what the internal wiring is. We have to guess. That terminal 2 is not a power source for the module. It simply is an exit for the PWR feed when the Body ECU thinks it is time to power up the windows, as in the key is on or during the magic 43-second stay-on time after the key is turned off. It is either a mechanical mini relay or its semi-conductor equivalent. In either case, 12V+ applied to T2 in the off state should just dead end there. But, without circuit details, I can't be absolutely sure.
Third, I don't know about the draw from a full-time bypass. The master switch is really a computer module, and it may have a very small power draw when not in use. I doubt it, but again, I can't see into the black box. It's easy enough to measure once you have done the mod. Even if there is, it would be the kind of thing that could go a few days before it drained a battery.
My suggestion for a non-permanent by-pass is find a dead relay, or sacrifice one, and pop the case off. then wire your by-pass inside the relay and put the case back on and install. One option is the mechanical approach where you simply wedge the contact arm in closed position. Then if you want to reverse, just swap the original relay back in.
Note that none of this applies to the liftgate window. That just ain't happening in a '99 unless you run wires all the way back to the liftgate because of the '99+ multiplex interface.