Joe,
While this discussion is not "technical" in nature, blow down time/area affects how the engine runs in it's proper state of tune for each setup.
So, in our example, Yamaha opted to go with very small exhaust ports as compared to the transfer port time/area. The result was better piston ring support, good mid range torque and a sharp reduction in high RPM torque. In other words, OK performance for someone used to 20+HP dirt bikes of the time.
However, Yamaha did understand the exhaust ports well, even back then. They published data on the modifications necessary to make the bike competitive with the Honda's.
Simply taking an IT cylinder and modifying it to YZ port specs was not enough. Sure, it helped, but the exhaust port was still too small. Following the published Yamaha YZ port modifications resulted in the best of all worlds. Good power, clean running, and much more fun.
Chris