The game is simple, but complete. It doesn't seem to have bugs and is well polished (but not very optimized for low level systems, despite how simple graphics is). Overall it's fine, maybe a little simple, as the gameplay consists of drag and drop of physics objects.
Theme of cross path is vague, but it fits. "In a Song" diversifier is implemented in the most basic way, but it's there.
Unfortunately, the way you claim to implement the other limitations is at least hacky, but some are just not there, despite the claims.
For example, having levels be saved after you finish them, doesn't constitute a checkpoint, because then you could argue, that saving the game in principle is a checkpoint too, which it isn't (checkpoint is a point in the level you reach, which acts as an automatic save point and saves you replaying the whole level from 0 (you are brought back to the checkpoint instead). The reason it's called a "checkpoint", is because you need to "check" it (set a flag). Well, if you need to beat a level to set a checkpoint, then that's not a checkpoint.
The graphics is a tad bit too complex for "Shapely", as it features complex geometry (conveyor model, bottles and grass are the most obvious); you could've gone with simple shapes and icons and made a match-shape-to-hole game, which would've fit the diversifier more, while not changing any logic. Also, colored lighting seems to be able to disqualify too.
"Two Buttons" is violated, as the rule states, that screen position or analogue controls are not permitted. Since in the game, you can drag an object anywhere on the screen with mouse, that's a violation (a solution would probably be to make a two button controls, which would push the front most object to left or right; or just not claim the diversifier).
So yeah, sadly, that somewhat tanks the score (if you didn't claim Shapely and Two Buttons, that would've helped; but the main issue are required, but missing Checkpoints).