Talking about header flanges, I cut the bars between the ports. I have had very few leaks doing this. The header companies weld the tubes to the flanges and grind the welds (not surface them so they are all parallel and flat) By cutting the flange, it isolates the ports from the others in case there is any warpage. Even cheap thin flanges can seal
I have TTI headers, and like you describe the flanges are one piece all across. It seemed peculiar to me, but I didn’t want to go cutting into some really expensive part without knowing whether it would help or hurt.
