This may be of interest:http://youtu.be/mEXGIIzQe6k
My speculation is that the rectangular signs, as well as the octagon stop sign, require just straight cuts and rounded corners which are much easier to perform - and the same equipment can be used for different sizes of signs.
But each cutout route marker - and advance railroad crossing sign - requires a special die cut, for each size of sign. And since there's only one sign that uses each die, the cost of the die and the cutting equipment cost can only be amortized against the cost of that type of sign. Throw in that there are much fewer quantities of those signs...well, those cutout signs start to get pricey.
A 12x18 "No Parking" sign can be had for about $15. Simple, extremely common. A 24" stop sign, about $30-40. With those signs, the increase is cost is mostly due to which reflective material you want. The higher reflectivity and more durable reflective material, the higher the cost. A sign suitable for a private parking lot or corporate campus (where reflectivity is not a main concern), inexpensive. But a 24" cutout sign is around $75 or more.
True, you can sell the scrap pieces, but that won't result in a large amount of money and certainly nothing that would come close to recouping the cost of the more expensive sign. Frankly, I'm surprised the U.S. hasn't followed Canada in developing a diamond shaped railroad crossing sign, or allowed a circular image on a square sign (much like the non-cutout Interstate shields ODOT has started to use).