A plumbing supply house may have a machine and be able to make you a nipple any length you need, and, they may have a larger selection of lengths. Worse comes to worse, you could buy a die and a longer nipple, and cut it then thread it to any length you need. A die and the holder isn't all that expensive, and may be cheaper than having someone make it for you. Since you may only do this once, you don't need a pro quality die. Harbor freight comes to mind, but you may have a local source that's similar.
Some manufactuers require things to be VERY specific positions for the fixture to fit right. Kohler is famous for this. Ever tried to get the threads within a 1/16" in relation to the finished wall with tile? It's tough, but some of their stuff won't fit right unless you do.
It's always best to fit things up before you actually lock the plumbing in to a specific location. This takes cooperation between the plumber and the guy doing the tiling...if that was you, you dropped the ball!
You could use a diamond core bit to enlarge the hole around the showerhead fitting so you could install a coupling. If the tile is properly supported, you could probably break it with a sharp chisel, but that can be risky. A Dremel tool with a diamond bit could be used to ream it out, but it would be dusty and slow. that would give you about an 1" or so additional length and may work, depending on the length of the horizontal arm of the arm you have.
You may be able to exchange the tub spout for one that is a slip-on verses a screw on version...that gives you more flexibility on the length, since no threads are required at all on the tub side...just slide it over the exposed pipe end, then lock it in place with a set screw. Most manufactuers make both versions, but not all.