Not defending the 40mb limit at all since it was clearly bs but... if he knew he didn't want to work with it... why did he?
Maybe there was pressure from the publisher or they just had bigger expectations ...or something.
For example, here are two different sides of a coin:
2010:
-Beamdog announced MDK 2 was coming to WiiWare
-Shin'en released Jett Rocket on WiiWare
2011:
-Beamdog released MDK2 on WiiWare (and MDK2 HD on PC on their own)
-Shin'en released FAST on WiiWare and NanoAssault on the 3DS (retail)
2012:
-Beamdog says "We dont' do Nintendo development"
-Shin'en releases a digital eShop (3DS) game with 2 more games coming this year too and announced support for the Wii U.
But goes to show that when developers commit , limit and hazzles aside they don't have problems with it. They may not be happy with said limits, but doesn't' mean that the limits were forced on them; since they chose to make those games.
So, that's why I guess the WiiWare version of MDK2 may have to do with Interplay. Since I don't' see Beamdog going and decided to port the game with said limits and sign the contract with that kinda of payment; when they released the HD version on their own digital distribution site for PC