More likely that's just similar sloppiness. Bujold didn't remind them about it, so they didn't do anything about it. Does she know about the ISOs on baenebooks.com?
I definitely think it's sloppy that the promo CDs are limited to the first hardcover printing, but there's no limit when it comes to the ebooks. It's probably fine in practice because most people don't know it's there, what it is, or have a clue how to use it.
I'm sure you're correct and Baen wouldn't want to act outside their rights. All I'm saying is that they acquiesced to Bujold's wishes. If they didn't feel they had the power to override her (even for non-legal reasons), you'd hope they'd try to avoid the embarrassment in advance.