As has been already said, your garage doesnt know what they,re doing.
The transfer box only has 5 seals on it !!. The 2 output shaft seals, the front and rear intermediate shaft " O ring " seals, and the main input shaft seal.
If you,re brutal enough, it is easy to bugger a new input seal when re-fitting the transfer box, but you shouldnt expect this from a LR specialist.
Siliconing the main box and transfer box together, as JM says, is a proper bodge job.
You can see here that this was done on this car.
They also sealed up the weep channel on the left hand side, so that if a leak occured you wouldnt see it.
You MUST take your car somewhere else. Taking out a transfer box and fitting new seals, realy is very simple stuff for a garage. It also sound like they have pushed the oil seal collar too far in on the gearbox mainshaft so it is not catching the seal properly.
ALSO, it sounds plainly obvious to me that you have a warped exhaust manifold, ( very common on the TD5 motor ), and NO amount of new studs and tightening is going to rectify this, The manifold needs to be taken off and skimmed flat, then refitted with new studs or better still, a Wurth stud kit.