is there a difference in blue? like its easier or you can skip jumps that aren't possible in yellow?

To my knowledge of running, no its just preference most of the time. Other runners might know something though

The only difference is that the redstone/commands blocks are not quite symmetrical underneath, but that is only minor important for With Exploits category. For normal runs I don't think so unless talking about saving small video time between courses in All Courses.

Through th some research there is only one block missing and that's a block