I am inclined to agree with OP's theory of the present time and 'space bubble' of the future being connected in reality. The position I take is this:
Izzy writes a novel for which the ending is not written (Tommy awakes from the reading to the blank pages). Despite the ending not being written, she has the idea for the ending planned, as she states 'it starts there....but it [ends up relating to Xibalba]' (paraphrasing, dont know the exact quote). That is, Izzy feeds Tommy lore about her historically-based novel in which Xibalba was a means for rebirth. Using this--and by curing death, as he was so adamant to do--he was able to live long enough into a future where he could pilot the bubble into Xibalba.
This has the following additional speculations:
The seed Tommy put upon Izzys casket at her funeral ended up being the tree that he took with him in the space bubble--a reasonable link between how the tree can be related to Izzy.
Tommy wrote the ending of her novel during the space travel. Evidence: If Tommy already continued Izzy's novel with the Conquistador reaching the Tree of Life and subsequently being consumed by it, (for lack of better description) there is no reason the story should then continue to an unrelated, as-of-yet-unmentioned character of the same likeness to go into space with the tree. Therefore, I propose the theory that Tommy cured death and then took the "tree of Izzy" into space. Knowing his long journey ahead and his physical looks, he finishes writing the story, interjecting the space traveler version of himself in the Conquistador story, allowing a ultimate parallel theme to the movie: Izzy dies...Tomas dies. Izzy the tree dies, Tommy the space traveler dies...
In other words, while any version of Tommy can defeat death (immortalization via the tree of life or immortalization by curing death), its the heart--the dedication and passion--and loyalty to her that is paramount.