Yea - that crossover is a bad design. I wheeled my old Tacoma for years without hitting it, but it's your call whether you want to go custom. Or get a full belly skid plate from somewhere like Budbuilt and you'll lose an inch or two of clearance but the exhaust will be out of harms way.
1976 FJ40 - green and mostly stock
1996 FZJ80 - not so stock