Wouldn't then 3 pin connector just fit on the 2 pin header but have the tach wire not connected to anything?
You could also just slice the 3 pin connector with a sharp knife to remove the extra position.
Is the 2 pin connector different to a normal fan connector? Sometimes they'll use JST XHP-2 or PHR-2 to save space. The XH are commonplace in electronics gear and the PH are used on GPUs.