I thought that the end of season 8 made it clear that the parts in the Reach Engine were Church’s experiences in the epsilon module. He touched the module, didn’t come out, then we got the zoom through the computer databanks, and it faded into the Reach Engine rendered section where Church talked about how “if you have to live in a memory, might as well make it a good one.”
So, I’m assuming this season:
Reach = Church’s experiences in the Epsilon module attempting to find Tex, and the experience is based on his memories, but some things are out of place due to his memoires being messed up (Doughnut giving orders), and he realizes this and attempts to correct it.
CGI Parts, like at the end= Church’s memories of the Freelancer that he uncovers as he relives things in the Epsilon module, which will most likely reveal things about Tex, which will make it easier for him to find her in the Epsilon module.
And if we get anything done in the Halo 3 engine, I think it will be safe to assume those parts are what is going on in the “present” with the rest of the crew outside the Epsilon module, like at the end of season 8.