Why the need for special 747s? Can't they put each chunk into a shipping container sized steel box and seal it vacuum tight, then ship that with regular 747s?
Splitting some of the parts into smaller parts will expose the insides to outside air which brings some serious cleanliness issues. The mirrors especially will get destroyed instantly by heat if there is any dirt on them when they are flashed by EUV.
I imagine they do the disassembly and packaging in a clean room. (At least for now the technicians require air :D) Then the packages are vacuum pumped, sealed, then shipped. Then at the destination fab they are assembled again in a clean room.
If I remember correctly, the machines are designed to fit the plane and vis-a-versa. So they will be smaller on top to fit the curvature of the plane body, for example
I suspect their equipment is susceptible to vibrations on a regular 747. I bet most of what makes their 747's special is dampening. Also, packing and unpacking the equipment increases the chance of things going wrong.