That's why there are regional averages. BiH Croats are Croats like any other and should be included in overall Croat average, it's ethnic average not country related one.
Just like Csango and Szekely are included in Hungarian average.
Most people don't have interest in some Bosnian average as it means nothing, it's just a country and not an ethnic group.
All 3 people in BiH are similar anyway.
Serb new average is made of Serbs from many regions/countries also, with western Serbs dominating.