I don't "mods" were ever really the issue with the Bethesda games, the reports seem to suggest it's more to do with how Bethesda were wanting to handle those mods. I don't thinks mods will ever really be an issue but like everything else that releases on consoles there are certain that you agree to do when you choose to release games on that console.
As a publisher, if you're not prepared to do those things then you're always going to have issues.
Well yes. Mods have traditionally been the responsibility of the user even when the company officially supports them. The only exception is occasionally a mod will be so good the devs will endorse it and help work on it like some of the VtM:B work. But even then it is an additional download you are responsible for troubleshooting. Sony is basically going the opposite of pc norms. Which might not be a problem for some games but would be very different from Beth's usual protocol of letting users do whatever they want and only removing things do to user response.