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Note: This is a provisional answer since I need to find support from books / journal articles about Aquinas's view of the new heaven and earth.
On the surface, the incompatibility stems from Aquinas's theory of the quality of the world after judgment (Suppl. IIIae Q91 Article 5) which seems to contradict Biblical description. But given that even the Biblical description itself is most likely metaphorical, Aquinas probably meant Article 5 to be within the realm of speculation based on Aristotelian/medieval cosmology that is now outdated.
The more pertinent concern that has a much more solid basis in Aquinas is our soul's relation to the Beatific Vision and to the new heaven and earth where our purified soul will be able to enjoy God more directly in heaven, and after judgment day through our glorified body also. There is no contradiction here, because in the new heaven and earth the glorified body is an extension of the soul that already had beatific vision after death (though needing purgatorial phase). The Catechism clarifies this point, which is consistent with Thomist teaching of beatific vision for the soul.
The remaining issue to be resolved is squaring Q. 91 Art 5 with the Biblical description of the new heaven and earth, which I think is secondary to Aquinas's account of the Beatific Vision, and even if it is irresolvable we can categorize this under Aquinas's outdated Aristotelian-based cosmology.