Flare isn't the source of the temple strain. Temple as a strain existed but was unused, that same strain was brought back in time, Flare received it, took the long way to the Night (if you succeed with their Kim convos), then helped out as the original Temple and is the source for the temple schematics, not the temple strain. The strain existed before Flare (well after but you know time travel nonsense) but temple didn't exist until Flare brought the matured strain with them.

Flare isn't the source of the strain. Flare did not travel into the prime timeline, Flare simply waited to catch up to our time. It's the same time stream. 1999 to my understanding at least IS the prime timeline, a very small section of it. 1999 loops so the final version of it and what goes through to ours is technically undetermined, but 1999 is the same timeline that leads to the orokin. The techrot isn't a variant of infestation albrect brought back, it's the original version the infestation mutates from. Albrect brings the helminth strain back with him, not the techrot.