While I haven't read the complaint and am not informed on the specifics of this case, I agree that under the parent commenter's logic, there'd be no commercial benefit to paying for R&D. If you're going to pump the cash into R&D, you have to be able to net something from it. R&D-type guys are going to have many varied interests, and it's certainly advisable that they create a hard, impermeable separation between things that they want their employer to be able to claim, and things they don't (i.e., don't even think about projects that you don't want your employer to claim while you're on their clock, in their building, or using their mail servers).

It may be that Carmack was used to there not really being a major distinction between what he owned and what id owned, and got caught off-guard by ZeniMax's insistence that this was a ZeniMax-only kind of thing now.