When he was far away from Earth and turned back, he was not in an inertial reference frame. He moved through various IRFs to this effect:
Before he turned back, he perceived his twin as aging slower.
After he turned back, he still perceives this.
Before he turned back, (He leaves Earth from his perspective) and (He leaves Earth from his twin's perspective) were simultaneous events.
After he turned back, they are not. This is because of the relativistic definition of simultaneity.
After he turns back, he is in an inertial reference frame such that t=0 for him is t=x for his twin, a nonzero number.
His twin perceives his journey to take, say, 8 years, while the twin aged 10 years.
He perceives his journey to take 8 years, which means that from his point of view, his twin should have aged 6.4 years. However, after he turned around, his brother's clock
has started at 3.6 years in his new IRF- so his twin has ultimately aged 10 years.
Note that nowhere here have I used the concept of a "universal" IRF to which either one is compared. It's the acceleration that changes the starting point in the IRF.
Now, this raises the question of why the IRF did not significantly change in the initial and final accelerations- that is, when the traveler took off and landed on Earth. The answer again has to do with simultaneity, which has to do with both the IRFs of the two events and their proximity. Two events that occur at the same place will always be simultaneous.
For further reading. Thanks to Battuta for explaining this originally and linking to some very helpful material in the FTL thread.
Although honestly I don't see how this discussion arose at all since neither a crane or a Herc is capable of withstanding the kind of acceleration that would be required to attain relativistic velocity inside an Orion hangar.

[EDIT] Ninja'd by watsisname, who is also correct about the IRFs.