The mechanics of time travel are consistently shaky in most fictional universes, but The Flash takes it to a whole new level week after week.
Barry’s decision to essentially steal the Flashpoint timeline for himself was an inherently selfish endeavor, and the erasure of that timeline from existence (when he freed Eobard Thawne) could’ve easily led to an angry and bitter version of himself.
Beyond that, going this route seems like great way to tie the entire narrative of the season together to remind Barry of the ramifications of his initial decision to save Nora Allen at the end of Season 2.
Season 3 of the Scarlet Speedster’s solo series has gradually moved away from the timeline-altering Flashpoint as a major plot point (particularly since the introduction of Savitar), but making the God of Speed a displaced version of Barry from Flashpoint makes plenty of sense.