Now its hard to see what the point was of the Shuttle, but if you look at the original retail prices of PC Engine systems, it all makes sense. Released two years before the down-priced Core Grafx II, the Shuttle cost 18800 yen, where as the Core Grafx was 24800 yen. The Shuttle was for gamers that would never eventually buy the extremely expensive CD add-on. Since they wouldn't be using that functionality, they weren't go to pay for it either so the price was lowered by about $50 USD, and the functions disabled. Then system was modified to look like stand-alone device, rather than a chunk of something (the original PC Engines).
This sort of thing is done all the time with, say, multi-core CPUs. Several of the cores will be disabled on the budget ones because making an entirely different chip for them would actually bring the price up, not down.
This happens with automobiles all the time with accessory and powertrain packages also.