If anyone's wondering, the answer is "yes, but can and should are two different things." Should have done it at a machine at a JR station. At the HND office, I got someone who managed to mess this up while managing to be incredibly condescending in the process.

First mess-up: Charged me the fare and reserved seat charge together even though I indicated when I first made the reservation that it was supposed to be reserved seat ticket only (my AmEx has an FTF and while it plays nice on sites like Eki-net that require a Japanese billing address, I'd rather pay the fare with a card that doesn't have it).

Second mess-up: Printed me reserved seat tickets from Kyoto when I'd booked from Osaka, even though she got that part right the first time.

Third mess-up: Properly printed my reserved seat tickets from Osaka back to Tokyo, but refused to acknowledge the first mess-up when I asked why I was only given one void slip from the 17700 yen charge for the Kyoto tickets when I clearly remember a 43000 yen charge from the first mess-up. It was only after I asked what slip she stuck behind her that she handed it to me and apologized. Also, my tickets now have a 乗変 marking on them.

Lesson learned.