I don't know if it would be relevant for a 4Runner, but I do remember having an issue with a different sized spare on a Jeep Cherokee. This was about 20 years ago, so I probably don't have the details correct.
We were driving my buddy's Cherokee, not the Grand Cherokee, on a trail to get somewhere. I believe his was full time 4wd and he had it in a locked mode, maybe similar to H4L in the 4Runner LE or perhaps he was even in low range. Anyways he hit a rock and destroyed the sidewall of a tire. His spare was slightly smaller than his other 4 tires, I don't remember by what but he had all seasons on and not AT tires.
We finished up the off road portion of the day, and when back on road the Jeep would not disengage the 4wd lock. This was before cell phones with Internet and we were many miles from home, so we got on the FWY. Even at under 60 MPH you could tell something was wrong with the drive train and the Jeep was not happy.
We decided to pull over and try to get it out of lock mode, the only way we could get it to come out of lock mode was to go from Forward to Reverse back and forth several times under power.
So perhaps if you are off road in 4 Low or H4L and have to change to a different sized spare you may not be able to disengage the differential lockup or get back into normal driving mode.
Please be kind, I just thought I would relay an experience I had in a different type of vehicle that is probably not relevant. When/if I downsize my LE wheels from 20 to 17 inch I plan on doing all 5 wheels so I can rotate all 5 per the manual and not have to worry about size differences.
