No, this issue isn't just a matter of "personal bests."
A biological male beat a biological female who is already an Olympic silver medallist.
The Olympics are already allowing biological males to compete with biological females. It seems clear that it's only a matter of time before Thomas knocks a deserving woman out of contention for a spot on the Olympic swim team.
Most of the defenders of trans women competing against cis women in women's sports inevitably fall back on the argument that the trans women don't always win.
It's true that Lia Thomas had the sixteenth fastest time in recorded American women's swimming history in the 500 meter freestyle. Again, Thomas was ranked beneath 400th as a man and just won a national championship.
I'm not trans, I'm just not a great swimmer, there are probably more than a million cis women who would beat me in that event. That's not the issue. There are probably several million men who would easily beat me in that event.
None of this changes the fact that biological men have an unfair advantage.