There is one matter which disagrees with your theory about Isaac Jones being married before he married Miriam, that is he states he is a bachelor on the marriage certificate in 1861. He married Miriam showing that, plus he was a Fisherman living in Gogarth Wydfyd. His father was Hugh Jones, sawyer.
I agree that having been born c1808-1813, Isaac was likely to have been married before but cannot find anything for him such as an earlier marriage.
I seem to remember that when I was searching for Isaac, there was another Isaac Jones around at that time, that is unless he lead a double life.
The whole situation with Isaac and Miriam needs quite a bit of research to establish the facts surrounding them. I am surprised a local historian hasn't done a study of them.
Re the church records, it varies from church to church. I have seen the mother's maiden name entered in the baptism register in some places. Some of my ancestors from Ysceifiog, who are in the baptism records there, have the mother's maiden name, plus her parents' names and where she originated from entered in the record. That was back in the 18th century. It makes it so much easier for genealogy many years later.