Re the charge my dealer is same way, 1 hour labor per flash. It sucks but it's probably more of a "dissuade folks from doing upgrades themselves vs having the dealer do it" deal. For instance if you had the dealership install the trailer brake controller (1 hour labor), the flash is included in that charge.
When I had the backup camera installed, it was 2 hours labor, which includes the flash. Now, it wound up taking them 1.5 days to do it, because they said the wiring was much more involved than they thought, but they still only charge the book labor rate of 2 hours. Actually, in my case since they took so long the knocked the labor down even more.
So, if you don't use the AlfaOBD or other similar tool yourslef, and do depend on the dealer for this stuff, anything that is 1 hours book rate labor it's usually same price just to let them handle the install as the flash is included.