Imagine how you would have felt if you were the only girl in the school who was not allowed in the girl's toilets because people thought you didn't look right. Imagine the sense of shame and isolation.
Girls with 'anomalies' with their bodies as you call them aren't excluded from the girls toilets. No one cares what size or shape your genitals are in the toilet and girls don't spend time studying the bodies of their peers whilst getting changed for PE.
This is not what you are framing as the argument though. A trans girl is male but you are conflating this imaginary scenario with a girl who looks different and is therefore treated differently. All girls look different from each other, as do all boys, as do all men and all women.
You appear to be saying that separating children by their sex for the purposes of going to the toilet or changing for sport is 'exclusionary' and would be bringing shame and isolation to a male-bodied child by not allowing them to change with the girls. Or are you saying that all girls should look the same so there is no confusion about whether they are a girl?
It's clear in this imaginary scenario you are prioritising the feelings and desires of the male-bodies child over the girls. I'd like to say I wonder why that is but I don't need you to explain it any further.