Even if we are accepting that as true, that doesn't really have anything to do with an individual patients treatment plan. You aren't evaluating risk based on the general population, you are evaluating risk based on patient populations with the same diagnosis.

If any risk is mitigated with gender affirming care compared to patient populations who aren't receiving care , and the risk of harmful side effects are minimal then the treatment plan is valid.

I don't really see how you think that comparing them to the general population makes any sense?

That would be like someone saying that people receiving treatment for HIV are still more immuno compromised than the general population.....well yeah, but treatment vastly improves their total outcomes.