As for the whole Johnson thing:
It's not cannon, cause in the novels we find out he survived by getting away on a Pelican. It was added in for fun. As for the Halo 3 Legendary Ending, it's not considered part of the Haloverse cannon (technically) until Bungie releases explicit info. on how it's part of the story. Therefore it could be (or not) contributing to the Halo: Reach story in the form of a time traveling Master Chief*. This belongs more or less in the regular Halo Forum, but I can see why it's in here now.
*I do not, in any way shape or form, support this theory.
~Hunter
[Edited on 06.14.2009 11:01 AM PDT]