There definitely can be a significant difference depending on how much total favor you've got at the shrine, as a single emblem's worth of fast learning is always equivalent to the first emblem's worth, regardless of how much favor that emblem cost.
Yes! I just donated and got an Emblem by accident ( i donated right before a new day and then right after a new day and the game decided it all happened on the same day). Instead of the 4 hours I would have received of off learning Metalsmithing for using 1500 of my possible 1700 Favor, the resulting Emblem is only worth 2 hours and 46 minutes. Not a very good option!