I also think Advanced doesn't mean "superior", but rather, "more difficult to integrate into the basic/core or will outright replace core mechanics".
An example might be splitting HP into two pools: A real wounds pool and a fatigue pool. Healing assumptions would change, damage assumptions would change (cone of cold does fatigue and hp dmg, e,g), class features would need to be re-examined (like a Paladins Lay on Hands - heals hp, fatigue, or both?). A lot of this would have to be decided at the table, that is the "module" won't cover everything. There would likely be corner cases, how a class feature interacts with a feat and this new thing called fatigue, that DMs would have to discover in play and deal with.
In short:
Basic: A Stock Ford Mustang. You have some dealer options.
Standard: A Ford Mustang Cobra. You have some dealer options and Cobra options.
Advanced: I pulled the engine on the Cobra and dropped in a Hemi. I also painted it Pink and put in a retro eight track. It runs on Bio-Desiel. People think its a peice of crap, but me and my family love it! Fully customized ride.