Yes, those are good points. The proposed dates of John's ministry are tied to these civil entities that have their own traditional dates, which seem to cloud issues rather than clear them up.
If I remember correctly, there also seem to be hard problems surrounding Augustus' decreeing the world to be taxed at the time of Jesus' birth. Trying to figure out how many such decrees were issued, when those decrees were given and when they were eventually implemented in Judea is a bit a puzzle. Also, nailing-down the year of Herod's death is not straightforward. The only thing people seem to agree upon is that Herod died some years BCE.
Yes the death is given between 4 and 1, a wide range. 3 people were supposed to get Herod's divided kingdom. The same 3 are mentioned in the ministry of John the Baptist. So 30 years later, they were still ruling. Allegedly the date of Herods death is in controversy, because the 3 wanted to be ruling before Herod died, to get "his authoritative blessing". If they started to rule in 1BC, then Herod died before that. Changing their rule to before Herod died in 1BC to 4 BC cannot then place Herod's death earlier to force Herod to die before their reign started. That is a self defeating argument.
Also the point of saying Jesus had to be born 2 years before Herod died is also pointless. Herod based the 2 years on when the wisemen first saw the star. Herod never new they found a young child. Also it seems that Joseph never took Mary back to Nazareth, but instead they fled to Egypt. It was probably only a few months after the birth, when the wisemen found the family. The star appeared 1 year prior so the wisemen had time to travel from the east. "Young child" does not mean Jesus was already 2 years old.
If Gabriel is the star they saw, Gabriel appeared more than 9 months prior to the birth to let Mary know she would be pregnant. I doubt it takes 2 years to get from India or even China to Jerusalem on foot. If it took a year, and they started 10 months before, Jesus was not more than 4 or 5 months old.
Even if Herod died in December of 4BC, Jesus could have been born in the summer of 4BC. I put the birth in 4BC. If Herod died in 1BC, that only means they did not leave Egypt before Jesus was 3 or 4.
Claiming a 3 year difference in Herod's death does not necessarily move the birth of Jesus 3 years earlier.
Many reasons are given why Herod was killed. Should not killing hundreds of babies in and around Bethlehem be at the top of the list? He had already made several wills and named several successors. Even the 3 that were given power were named prior to his death. Yes, he had tried and succeeded to set up a few choices as rulers, and then killed them off. It was not out of character to kill innocent people, and that is why a few decided to end his life.
Both dates are fine with me. I think Herod still could have been killed only a few months after the Bethlehem incident. Jesus' birth does not need to be moved to 7 or 6 BC.
The only reason the calendar is even off would be because the date of Nisan 15 in 33AD landed on a Saturday. The church thought at that time, still does, that Friday has to be the day before Passover and the same day as the Sabbath. They do not follow Scripture that indicates they were not the same day that week. So the first year, represents 33 and a few months to April as the 33.5 year life of Christ. Much later scholars went with a 30AD date that did separate the Passover from the Sabbath, thus sending the birth into 4 BC.