To get back to that jumping thing:
Do you think it would be better if you can jump invisible? How would you be able to control that? Golden Tail doesn't even force you to make the highest possible jump to progress (there's always a platform nearby to make thing easier); but if you learn to control that jump, the game is more fun as is a bit harder.
If jump is restricted to the start of the magic you can calculate where you want to jump. It takes practice, of course. Also the magic not only allows you to jump higher, it makes you fall slower. And you get that with practice.
I believe it would be easier, more predictable. the "magic" button becomes a teleport button: if you implement an acceleration after a visible jump, you give the player a higher jump without removing their visual clue to time the jump right. it would even allow for even higher jumps, giving you one more gameplay trick, for example like using the magic at the apex of a jump to reach even further than a simultaneous jump+magic.
Or as something closer than what you already done, where the magic is fast-tracking invisibility: momentum obtained before the magic is kept but not accelerated, only the momentum built in magic invisible mode is faster. But in that case, you can't limit jumping to exactly when magic start. If you can start moving left and right after having pressed the button, you should be able to jump. No matter how dangerous it is for the player.
Jumping while invisible would be just something the player would have to learn to avoid (which is easier when jump is FIRE2 and not UP), or would want to learn to master, like if a monster is next to a ledge, they would want to use the magic just a moment before jumping, to try to reach the ledge before vaulting. and if they miss, too bad, they fall down. To the ground where they can then climb up and try again to get the timing right, or try differently.
As of now, it makes for a gameplay that is more static: the player instinctively stops before a long jump to time the inputs correctly, instead of doing a more natural run and jump.