Your question asks:
What are the key differences between something having real game dynamics and simply being a superficial gamification layer?
When designed and implemented correctly, Gamification does include real game dynamics:
- There is a strong focus on rewards, but those rewards must fall within a balanced system.
- There must be engagement.
- There must be motivation (both intrinsic and extrinsic) there has to be levels to complete and accolades/rewards delivered upon completion.
- It should be fun, so "play" is a focal point.
- Risk factors must be vetted.
- Play challenges must be developed, and remain balanced.
The problem with gamification is that it isn't taken seriously from the outset. It is usually seen as marketing afterthought. It is often developed by marking persons with little knowledge of game dynamics and more focus on "social shares" and "badges given".
The bandwagon of "Gamification" is produced by many, but refined/balanced bby a few. The many that fail often give the few good examples of it a bad name.
You also asked:
Where is the line between a serious game and an application with points?
You would need to define "serious game" in order to answer this effectively, however, I will go by an assumption you mean a AAA title from Ubisoft, Nintendo, Bioware or the like.
A serious game has level designers, programmers, story developers, character arcs, modelers, script writers, designers etc. They are focused on the dynamics of the game-play and making sure not only is the "look and feel" of the game is done well, but the inner workings of the game play dynamics are sound. A powerful weapon needs to be balanced so that it isn't a "god weapon" and a powerful enemy must be beta tested so that it isn't invincible.
Though gamification does not usually have the level of complexity in it's "design layer" there is a lot of insight and forethought put into a well designed system to maintain a fair and balanced game-play system.
The line that is drawn is in the level of complexity and planning that is invested into the gamification system.