A couple of things need to be sorted out:
1. When you say "Key / Fob". Do you mean rubber coated key? For "Fob" it would be the remote entry plastic fob with buttons.
2. The "Security indicator" would be a lit car logo with a picture of a padlock. This is the engine emobilizer logo. You will NOT be able to start your truck with pliers.
I have a 1999 so can't "know" what your dash or instrument area looks like. My key area simply has the lit ring and "lock, on and start" etched into the metal. I'd bet money your key has a chip. You can have it tested at any place, like Lowe's, that has a key maker. The machine can also test for chipped keys.
My vehicle also has etched Vin on ALL glass and a "VIP vehicle intrusion protection" stickers on the two front windows. And, "VEHICLE PROTECTION PACKAGE" sticker on the drivers side passenger window. It also has "PERMA VIN" stickers on both passenger rear windows. I also have the blinking light with the glass breakage mic on the lower left of the dash panel.
I say all of this to give you some indication of the protection level available from Toyota. I don't know what was "Standard VS Optional".
The chipped key, I believe, was standard after the technology became available. Can't be sure though.
None of this means anything to you unless you can find some other evidence for yourself.
Quick test. Lock the car with someone inside, wait about one minute and have them open the door. If the alarm goes off, starting the vehicle with the key will reset it / deactivate it.
Hope this helps.
P.S. Only use remote FCC ID HYQ1512Y...........HYQ12BAN is for the Sequoia for our model years.