I drilled holes in the end of my motad when I had one; It certainly helped a bit.
However, when I changed to my laser pipe I was amazed how restrictive the Motad had been, particularly in the lower end of the rev range. With bigger jets and after market air filters and a better exhaust there is definitely more power to be had but it does take three kicks to start up whereas before it would start after one.
Many years ago, on my CX500 I made a two into one system using flexible exhaust pipe from a tractor shop and a BSA Goldstar exhaust. Sounded great and worked wonderfully.
If you do modify an exhaust it is worth making carefull test runs to make sure the engine does not get too hot and experiment to get the jetting right.