That is infact the main reason modded beams would be better for jumping (clearance, not so much strength or travel #s).
However they don't come without a downside though, and that's increased jacking and track-width narrowing at droop that comes from having the pivot points higher up in the chassis (along with more stress on the center axle u-joint & slip-spline). This can affect some aspects of handling at slower speeds more than it does at high speed, particularly if you have to traverse an off-camber hill or rock at an angle instead of going straight up it.
My beams are not modded for lift. They are reinforced in a couple spots for strength however. While I don't normally do the jumping thing, I do find the suspension still handles the smaller undulations in the road far better than solid axles when I do pick up the speed a little.
TTB seems to work rather well in rocks, I've found. Pretty much any time I'm out wheeling it's with solid axled rigs, so a direct comparison is always available.
If you build a TTB to take on rocks, something you need to pay particular attention to is the springs. Almost every TTB suspension lift out there has coils that are literally twice as rigid as they need to be on a BII. This will totally make or break performance, as it of course robs you of most of your flex. The other thing is steering geometry. Again the aftermarket gets it all wrong in most cases (mainly all the mainstream companies).
I used Jeep Cherokee coils that are a bit on the stiffer side (for the Jeep anyway). These have basically twice the flex of TTB springs.
I also put a "center" limit cable on the front suspension (single cable that runs over the frame from one side to the other), which kindof further forces the TTB to act like a straight axle while the going is slow. But if you want to go fast, the cable can be released to allow the full independent amount of droop travel.
Although I built mine a little more toward the Rockcrawler side than Prerunner, I'd bet I could turn it into a good dual-purpose rig without much further investment (mostly with just putting a better shock setup on, as I've already got the travel). Jumping it really just doesn't seem to thrill me as much though (maybe it'd be different if I was 20 years younger

).
As for a prerunner looking goofy on the 'Con, I guess it's all a matter of perception. I wouldn't really see it as goofy myself, although some probably see my TTB as "goofy", that is until I idle up over that rock they kept slipping on in their Jeep lol.