If a formerly Male athlete is winning in the female competition then there will always be question marks over her.
I think you meant to say, "If a female athlete who was assigned male at birth is winning competitions then it is wrong to assume she would always win." There are cis women athletes who win more often than non-cis women athletes.
who identify as a different gender
"Identify" implies a choice that may be subject to variation or is somehow suspect. Rather, one is possessed, or is not possessed, of one kind or another of gender identity.
a person is pretending to identify as a different gender in order to gain an advantage.
People have always been able to do that. People have always been able to use the 'wrong' toilet, too, but most people don't because of social convention.
Some people probably have tried gender expression fraud in their sporting discipline. The nature of being an athlete – for this argument – is to be better than someone else by using one's physical advantage.
The core aspect to self-ID is that it removes the hitherto intrusive medicalism inherent in the process of confirming ID, and does so with certain restrictions that prevent or criminalise frivolous, fraudulent and/or repeated applications.
If it were easy, male athletes would spuriously show up in women's competitions with underdeveloped secondary sexual characteristics, wipe the floor with both unbridled success and a hell of a lot of self-confidence to face the media and competitors, and then suspiciously disappear to undo all that pretence. Except that they would be breaking the law because they would have originally signed their affidavit that said they wouldn't do that.
I don't want to start a whole thread about this, because it's a debate in which some people may not feel empowered to take part, and for anyone here who has no such advocate I also don't want to let this go unchallenged.