The parallel flag is indeed never set to true when the build is done in parallel.
However, there is a special consideration: the current MultiThreadedBuilder will only build in parallel when the degree of concurrency (determined with -T) is at least 2, and when there are at least 2 projects to build. So running mvn help:evaluate -T 3 on a single project (like the stub project) will still build the project with just 1 thread. In this case, which is the example in the description, I think session.parallel should still return false (and not true like Maven 3.0.5 does, in the given example): even though -T 3 was set, it is ignored and only one thread is going to be used, resulting is a sequential, and not parallel, build.
To me, the fix here is to have session.parallel set to true when more than 1 thread are actually used to build. MultiThreadedBuilder does not clearly document the number of threads used, but if we agree on this, I'll also add it to reflect that.