Yep...Its all to do with major diameters and minor diameters. You also have to take into consideration the thread pitch as Toyota thread sizes arnt always a standard metric pitch. theres a mix of metric course & metric fine.
Major diameter on a bolt is the peak of the threads, the minor being the troughs....a bolt hole when drilling a hole to suit, needs to match the minor diameter or there would be nowhere for the thread to go.
For things like the under trays, there are some self tapping bolts used which from the dealers are quite expensive, I picked up a bag of 200 self tapping bolts the same as Toyota for about £5 from an auto jumble, the thread pitch on these isnt critical as they will cut there own thread, (They usually bolt into a plastic but they do need to be the right diameter so they have enough grip...too small and they will drop out, too big and they split the thing they are tapping in to.