The last time I purchased a Japan Rail pass voucher from a travel agent in the US, it was issued like an airline ticket, on ARC ticket stock, and with a JL ticket number. The only thing I purchased was this voucher - there was no associated flight on JL. This was from a travel agent that specialized in travel to Japan. However, I would imagine that any travel agent that can issue tickets on JL would be able to issue this rail pass if they know what to ask for in the computer. Has anyone been able to accomplish this with a "regular" non-specialized travel agent that may not have done it before?

yes, that is how I did it. JTB (Japan Travel Bureau, one of the biggies in Japan travel) wanted to charge more for the Green car (1st class) pass than my "regular" travel agent wanted. She said it was easy to do.