To be a bit provocative:
While junior chess can be unwelcoming for girls, the main reason there aren't many strong girl players is that they have better things to do.
Almost all children decide they aren't interested in playing and studying chess at the obsessive level that is needed to stay competitive as they get older.
99% of boys decide this, and 99.9% of girls. It's a sensible decision. Unless you are a competitive chess player (I'm not either), it's the decision you took.
Given this, measures to ensure girls win chess prizes that they would not qualify for if sex were disregarded are pretty questionable. No it's not the worst injustice in the world. But none of the usual justifications apply either:
It's not like there is a great societal need to have lots of strong female chess players. If you need a chess puzzle solving, a computer can do it. It's not a representational matter (like parliament). It doesn't affect wider outcomes (like board representation). And it's not because it's a different game (like sports). Chess is exactly the same game for both sexes, and the main reason one sex doesn't do as well as the other is that, on average, they sensibly choose not to.