Often times in the old Czech parish registers, illegitimate births were recorded right alongside legitimate births. But, sometimes they aren’t.
For example, in the parish book “Merklín 03” on actapublica.eu, the births go from 1736-1770, and then at the end is a small section of pages of births of illegitimate children from 1769-1771.
So keep this in mind when you are searching for births of your ancestors! If you can’t find them in the regular section of the book, maybe try looking elsewhere.
As if there weren’t enough possibilities for places to search without this added variable! I wonder what the purpose or intention was of separating these births from the others; was it just another way to mark the women as apart? Was it somehow for the benefit of the children? Was it to make it easier for future record keepers to do look-ups for these children?