I am not an expert on the LR Tdi engine by any means but I am an retired diesel fitter/mechanic, by checking about I have been able to discover that generally the "code", by means of number of holes in the tag on the head gasket indicates the thickness of the gasket in increments of approx .1 mm, that is equal to about 4 thousands of an inch (.004").
It seems that if your engine originally was fitted, say, with a 3 hole gasket (the thickest?) and now is fitted with the 1 hole gasket (the thinnest), that will have moved the head surface .2mm (.008") closer to the top surface of the pistons, everything operates close to give the required compression to ignite the fuel and optimise output without parts colliding.
The above reason is why your mechanic should have carried out a "piston protrusion measurement" with the head off, (piston height above block deck), it is required to select the correct thickness gasket to avoid a case where the pistons can come in contact with the head surface.
A small amount of wear in piston wrist pins and big ends coupled with inertia can give enough over travel of a piston or pistons to collide ever so slightly with the head surface, maybe the source of your engine noise.
The fact that you supplied the parts may let the mechanic "off the hook", unless he was claiming to be a "Land Rover Tdi expert", there are many general mechanics out there who do not "get" some of the specific knowledge required for diesels.
So good luck with it, do not drive it too much whilst it is making the noise as it could lead to more serious damage, and getting your own parts is only a good thing if YOU are going to do the job yourself, at today's labour rates it can be no saving at all to buy bits and then get stuck with the labour costs to do it again because of failure to perform correctly of parts that YOU supplied.

