So after my mechanic/mechanics across the street tried to diagnose my issue a couple posts above, the conclusion was something to do with the immobilizer.
Because apparently remote start works 100% of the time, and with the key, it was working like 20% of the time. They didn't charge me for diagnose fee.
They couldn't test further because I only had 2 keys, and the other one is being used for my remote start (already buried somewhere deep in that kick panel)
So what I did is I bought these exact keys from eBay (
NEW REPLACEMENT TOYOTA 4C CHIP TRANSPONDER MASTER IGNITION KEY FOR 89785-26020 | eBay)
Then I used these steps to program them myself after my mechanic's friend cut the key for me (also no charge
)
2000 4Runner Key Programming Instructions
Worked instantly.
However, to get to the point, I didn't encounter the starting issue again, and it's been at least 2k miles.
But at least I learned something new and now have 2 extra master keys in case they need to diagnose further.
The only thing I can think of is that I was low on gas when they were diagnosing it (I think the low gas light was on) and when I picked it up, I filled up gas right there since it was the mechanics from the gas station across my regular mechanic. I did try going low on gas again to see if it'll occur but it hasn't yet.