The reason to use a flat washer under a split washer is to prevent the lock washer from marring the mating surfaces and digging in. One, when this happens and peels off some paint or powder coat, it's a spot for rust to start. Second it can cause the split washer to uncurl, losing it's ability to act as a locking washer. We've all see this, when you take one off and it looks like a crescent moon.
Anyway, look at all the fasteners Toyota used originally, they almost all have captured lock and flat washers, so it's not a random thing. I suspect the uber thick washer is to spread the load off the bolt head. Several of the bolts ARB included with my bumper had the same sort of thick washers. Shrug.
One thing is fer sure, if the choice was to use a flat washer but not have total thread engagement (e.g. making the bolt too short, so to speak) against using one I would leave it out. A bolt that does not full engage all the threads is asking for trouble IMHO.
"Silent enim leges inter arma." -- Cicero