The transmission doesn't "learn", nor does the PCM.
Does the center stop light in the cab roof work? That's also a player in the whole byzantine brake light / LED / pedal switch / TC lock-unlock melee.
I had an odd thing happen recently along these lines. It's a manual, but a similar situation. I removed the center stop light bulb a while back, because the truck has a topper, and that bulb gets hot. Only effect was, cruise control would interrupt when I hit the turn signal. The goofy way the truck is wired, that sent a dummy "brake pedal on" signal to the PCM, thus canceling the cruise. This is the equivalent to automatic trucks unlocking the torque converter when the PCM receives a brake pedal signal.
Couple weeks ago, cruise became inop completely. I checked every circuit, brake lights weren't stuck on, steering wheel switches all checked out, fuses checked out, yada yada. Finally I plugged her into AE, and sure enough, the "brake pedal pressed" (or whatever it's labeled in AE) was set to "1", meaning the PCM THOUGHT I was pressing the brake pedal. For S&G, I turned off the key, re-installed the bulb in the CHMSL socket, lit it back up, and the brake pedal (BOO) signal went back to "0".
For MONTHS, this was not a problem. I didn't actually monitor it, but I bet that previously, the signal according to the PCM would remain 0, and go to 1 only when I hit the brake pedal, or hit the turn signal. It was totally out of the blue that it went to 1 at all times that the key is on, and went to 0 again when I re-installed the bulb.
I don't have an LED in that denomination of bulb, so I don't know what impact that will have on how the PCM reads the brake pedal.
It stands to reason that it won't throw a code. It has no way of knowing the difference between a false BOO signal like described above and a real one when you press the pedal. Similar to when your CPS fails, often it doesn't throw a code because it doesn't know the difference between the failed sensor and the engine actually not turning.
In any event, while troubleshooting this, if you have a way of reading live PCM data, that would help. Set it to read brake pedal state, and monitor it as you fiddle with different bulbs, resistors, etc. The goal is to see it only switch from 0 to 1 and back to 0 based on the pedal.