Toyota has two factory alarm systems - the VIP RS3000 and the VIP RS3200. The remote you're describing sounds like the RS3200 remote, but a 99 4Runner would have to have an RS3000 installed. Maybe the newer remote works with the old system... I don't know. The RS3200 didn't work with the 4Runner until 2000.
The RS3000 has the limitation you're describing - if you arm it, you must disarm it with the remote. Normally that's OK as long as you have power door locks, as the system is effectively just like keyless entry - disarming it unlocks the doors.
The RS3200 can be disarmed by either using the remote or unlocking the door with a key.
The 4th Gen 4Runner (2003) got away from the VIP alarm systems and went to what we'd consider to be a normal keyless entry system.
Normally, if you lock the doors with the remote, you will arm the system. It also has a mode called "passive arming" which can be enabled or disabled; passive arming will also arm the alarm 15 seconds after you turn the key off if the doors are closed. That's disabled by default.
However, the system also has what's called "Valet Mode", which disables the alarm functions and merely acts like keyless entry. Interestingly, I don't see a way to get out of Valet Mode in the manual - there's only a sequence of steps to turn on Valet Mode:
1. Turn the ignition key to "ON" (not ACC)
2. Using a remote, press and hold both buttons for 2 seconds until the status monitor LED turns on.
-- You have 30 seconds to complete the remaining steps, or the operation is cancelled! --
3. Press and release the top remote control button 3 times. The system should chirp and the exterior lights flash.
4. Turn the ignition key to "LOCK". The system should chirp 3 times and flash the lights 3 times.
Maybe the same steps would turn off Valet Mode?
Here's a link on TundraSolutions with this info and the manual in PDF format:
Will I have issues? | Toyota Tundra Forums
As for location of the ECU, on a Tacoma the RS3000 ECU would be behind the left kick panel on the driver's side. That's one possible place yours might be installed.