or he knows that NSA can own both Windows and Linux. Which is probably true. At which point, he needs to 1) know his system is not yet owned and 2) that the encryption system he uses works and isn't backdoored.

So about his only plausibly concern is if Truecrypt uses the Window's entropy pool switched to use say EC_DAUL_DRBG. That is a concern, but it's one with Truecrypt and can be checked.

This is assuming that even for the NSA, having Window's identify and modify the truecrypt binary is impossible. Realistically, if you are worrying about that, you should worry about Intel chips doing the same thing. At which point, you're screwed no matter what OS you use.

Would add to this that he is in a sense a high value target by the fact that he is well known and has an agenda which others may not approve of.

What might not be practical or possible with "anyone" becomes "possible" with a high value target. [1]

I'm remembering back to OJ Simpson case back in the early 90's. The police did things to try to pin the crime on him (searching trashdumps) that they simply don't do or don't have the resources to do in ordinary cases. (They found nothing but they tried and went to an extraordinary effort to try and find some evidence against OJ.)

[1] I'm wondering for example where physically the air gapped computer is kept and the physical security and/or alarms around that computer.

Physical security is the least of his problems. You can mount a lot of tempest[0]/ attacks from across the street.

http://en.wikipedia.org/wiki/Tempest_(codename)

And -you- would know that your open source OS does not have backdoors and zero-day vulnerabilities and such?

Don't be silly.

So what if they can't access those?

Who is "they" and what are "those"?

Is "those" referring to zero-day vulnerabilities?

You realize that a zero-day vulnerability means "they" accessed "those," right?