Toilets come in different "rough in" sizes, generally 10", 12" and 14".

The measurement refers to how far the center of the roughed-in flange should be from the finished surface of the wall behind the toilet for the toilet to have proper clearance from the wall.

2" of space can seem like a huge gap, but it can be disguised. Or the wall can be built out a bit depending on the wall itself. Or you can replace your 12" toilet with a 14" toilet.

A 12" rough is pretty much the standard in construction.

Hi saggy,actually I prefer enough of a gap between tank and wall such that painting with a mini roller and/or wall covering hanging can be easily done. As well,ocasional cleaning is possible-no inaccessible dark space with mildew potential. I just checked one of my toilets-about the same 2 inches but the with lid on gap is reduced a fraction. My opinion, better a 2 inch gap than none.

"The 14 roughing leaves the 2 inches and the contractor said the 12 inch roughing is too tight and risks a leak"

Were 14 inches needed for proper flange fit with your particular toilet in this bathroom? They do make off set adaptors which can be set at 10," 12" or 14" in spite of your vitreous china bowl. Toto makes one, for example, in any of the three sizes. If this is the case, a 12" offset adaptor might minimize that rough in extra 2" space you don't like.

Perhaps you wish to talk with your contractor about this. Good luck.

Are you sure it wasn't done this way because of the location of the floor joists? Sometimes you want to put the pipes in a certain location, but the floor joists get in the way.