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Can't recall 100% but I think I remember the Russo Brothers addressed this in an interview. Thor was actually more powerful when he fought Thanos alongside Cap and Iron Man during Endgame.
They did say that, but the actual movies don't show that at all.
In Infinity Wars, Thor comes in at the end and essentially kills Thanos who has the full gauntlet, then in Endgame he and Cap get beat by Thanos who doesn't have any stones