This is what I've heard from various folks over the years—not stating this is fact, just what I've heard from people with various levels of reliability—@KIghostguy, @Shaggy, @TombraiderTy probably know more.
My understanding is that both Flight of Fear's ride block systems were designed to accommodate four trains. Clearly it never did and would've been a challenge, but I think theoretically—you could have had one train in the load station, one train in the "tunnel" between the load and unload stations, one train in the unload station, and the fourth train sitting on the safety brakes just outside of the unload station. I don't think, in that ideal operation, that a train would've had to sit at the midcourse regularly, but that would've required—the unload station to disembark guests rapidly and then quickly move that train along. Ultimately, a lot of that comes down to the main station loading and launching quickly—which even in the best of conditions takes awhile. Guests would've likely been sitting on the safety brake run for awhile (and then if things didn't move quickly, the midcourse could've stacked). Four trains would be hard to do.
In the end it didn't matter because they only put three trains on. And I believe after an incident with wooden coaster skid brakes in the early 00's, Paramount adopted a policy of trains needing to have an additional set of brakes between them. I.E. If you look at the train sitting at The Beast, waiting behind the station—there's an extra pinch brake between it and the station.
I'm not sure if this is correct. Dominion ran three trains for years while Kings Island ran two. Not sure if it's still that way now. I do know that for a time, a few of us had looked at KD's ridership data and advocated for KI getting a third train (especially after Fast Lane debuted and was a mess with the "fast lanes" only being slightly less longer waits than the main queue). I don't recall the LIM's being an issue, but I do know that maintenance did prefer having the third train at the ready and being serviced during the season. Ultimately, our FOF never got its third train back. Also, at peak operation—Backlot moves trains much quicker (thought not with as many people), I think the LIMS can handle it.
There were also operational changes over the years. If you remember the earliest days of FOF—the empty train entering the load station would come in with its restraints up and open. I believe at some point, that changed and if I recall correctly—the employee at unload needed to close the restraints and check them even if there weren't riders. The unload station train also can't depart until the station is totally void of guests, which originally I don't think was the case—guests just needed to be beyond a line.
RANDOM, SLIGHTLY RELATED QUESTIONS:
@TombraiderTy, @Shaggy, @KIghostguy, do you all know about "The Bat Phone" from FoF's early days? Also, did any of you ever hear about SOB and Beast being designed for four trains? And in that vein: did SOB ever run three?