@Lilliwyt Yes, I'd consider that yuri. Of course, it's different if they start to feel like they are the gender they swapped to (e.g. Kanojo ni Naru Hi), but the typical "I'm a horny 30 year old man in a 16 year old girl's body" is absolutely not yuri.
Somewhat related, I'd consider relationships between two women where one or both are trans to also be yuri (e.g. Aerial Magic), though that is exceedingly rare in manga.