I think multiple voltages and multiple signaling / PTC systems are both "solved problems", which makes me think there are three different reasons for the cost difference: North American equipment is just different than most of the rest of the world, there are less vendors and purchasers for new locomotives in North America, and (it seems to me) that locomotives are more of a retail kind of commodity in Europe.
The "just different" are, I think, two things in their own rights: different crash worthiness standards between the USA and most of the rest of the world that demand differently engineered bodies, and lack of homogenization between AAR and UIC practices, meaning that equipment that works in AAR systems does not work in UIC systems.
There are two major manufacturers of locomotives in North America: Progress Rail and Wabtec with Brookville, NRE, and RailPower as minor secondary players. I don't know where Siemens fits into this picture: do the recent Charger orders make them a major manufacturer in NA, or are they still minor beside Progress Rail and Wabtec? There seem to be only a handful of purchasers of new locomotives in NA: Amtrak, the Class Is, some commuter railroads, while most Class IIs, regionals, short lines, and remaining commuter railroads buy on the used locomotive market.
Europe seems to have more major manufacturers (even if owned by non-European firms): Alstom, CAF, Hitachi, Siemens, Stadler (I'm sure I'm missing others), and many minor firms that produce locomotives. It also seems there are more companies that purchase new locomotives, and many of those companies seem to have relatively small fleets (or are legacy national carriers with large fleets), and are likely to be in the market for a handful of locomotives at a time instead of in the market for large orders with complex option structures.
That large selection (lots of vendors) from a large number of small customers (lots of customers) makes the market more retail than the US market is to the point where Siemens developed the Smartron locomotive: customers can't even choose the paint color, and its sold on a standard contract, which does make it inexpensive to buy new. (This isn't to say there aren't lots of older locomotives running around Europe in daily operation either.)
I don't know if there are (or aren't) other incentive structures that are encouraging a stronger new locomotive market in Europe than in the US, but it seems there is a stronger market for new locomotives in Europe and that does drive down prices.