I was running into this same issue. I had turned off custom transaction numbers under Company Settings>Sales only to see it turn back on using the new invoice template.
I think I may have found a solution. It looks like the the setting is now also attached to the template. I you go to Custom form styles>Content>Header, then you can uncheck the Use custom transaction numbers option.
This seems to keep custom transaction numbers off for me, hopefully they stay off!
