The National level flag counter shows national flags, not regional ones. As much as many people in Scotland and Wales might want independence, they don't yet have it.
So, it makes sense to have the Union Jack as the National Flag at the main flag counter level.

Many of us have argued for Wales, Scotland, England and Northern Ireland to be shown at the regional level for those with the advanced flag counter pro.
Jeremy has not answered this request yet - we must assume he's working on it.