you pose a good point. that one nut especially if it has a flange and if the header was welded up in such way minimal clearance was left for the installed nut can be a serious bitch to remove.

IF you are unable to get a even a 3/8 or 1/2 thin walled socket on the nut without rubbing into the pipe your choices become rapidly circumscribed.

1. if the other 2 came off without drama there might be 'hope' that 1/4 inch drive deep walled socket might be able to slip over the nut an still clear the pipe od wall. you won't be able to get much torque using 1/4 drive but you may not need to. and if you break the socket succeeding its still better than the alternative.

2. which brings me to the alternative which is as you state, remove the exhaust manifold and the do the job on the bench. if you must go this route make sure you rap each nut with a cold chisel to shock them before loosening. use pb blaster and let sit a bit as well.

use 3/8 drive or less and turn each nut by hand in tiny increments until you know you are safe from snapping a stud. you do not want to break stud here. it will only add to your work and trouble.

i do not think you will have any luck trying to remove manifold to header nuts using any kind of wrench. no clearance to work.