HERE IS PROOF, this is Alan Bell, CEO of Paramount, answering a question about space:
PCW: What if the multiple soundtracks and high-definition bonus materials won't fit on a single disc?
Bell: If there's an overflow of bonus material, we'll just go to another disc. That's not an issue for consumers. In some cases, they consider that it has more value. It's done routinely in DVD. Why put every single title on a high-capacity disc if it doesn't need it?
As you can see, the reason has nothing to do with space, as they are offering a Transformers 2 HD DVD Disc set, thus leaving plenty of room on Disc 1 for TrueHD.
The fact that they didn't include it has nothing to do with capacity, it has to do with a decision within the studio determining that it simply isn't needed.