I mean, you've answered your own objection here. The number of trans people is extremely small. So creating an extremely small number of extra medals is really not much of a hardship.
As for creating "an entirely new category", this is simply in terms of record keeping. If Lia Thomas swims against female athletes, the only change that's required is a spot on the results table where her time and position (1/1 in this case) can be recorded. Neither of these feel particularly onerous to me. Do they to you?
As for team sports or elimination events, yes, that's more complicated. But I didn't claim to have a perfect solution. However it can be easily implemented in a lot of sports. And it's fairer, more inclusive, and less controversial than what we have now in the sports where it works.