Having owned a 1996 Land Cruiser, 2003 Prado and now 2012 GX 460, I assure you I've experienced this issue in all of these cars particularly that 1996 LC.
On the issue of paddle travel, am certain it has nothing to do with off-roading, but rather to do with countering the excusive nose dive during braking events. Emergency braking in Lexus GX 460 or even LX 570 feels dramatic when I compare it with my old 2005 Range Rover. Even more dramatic/hilarious when EBD+Pre-collision is in action, the whole car squats; absolutely no where close nor gives confidence as it's German rivals or the land rovers do.
It's a classic issue in most of Toyota's SUVs. You may get used to it .. but certainly in a stop n go traffic you will need to always keep the extra distance.