The upgrades/substitutions I am aware of:
Level 1: straddle sole circle dismount or underswing dismount.
Level 4: you can add a sole circle after the squat on.
Level 3: kip instead of pullover
Level 5: straddle cast instead of straight body, stalder circle instead of clear hip, layout flyaway instead of tuck, added sole circle, backhandspring or front walkover or backwards roll instead of back walkover on beam, front or side aerial instead front tuck, switch leap instead of split leap.
also, all kips and glides have the option of being straddled or piked, as well as squat ons can be pike on or tuck on.
None of the substitutions give bonus, but a lot of times either people competing them are already ready for the next level but are not old enough, or they need a way to work around a skill due to injury or mental blocks.