I found a pretty straightforward way of placing a warp pipe that leads from the start of the level to the middle. The player will not realize it is a checkpoint until they try going through the pipe on the other end and come out back at the start.

1) Place a pipe near the start of your level that takes you to the subworld. Screenshot 1

2) Drag 2 horizontal pipes on top of your warp pipe. Your pipe will still be there behind them, completely invisible to the player, but still usable Screenshot 2

3) Add some enticing elements to the right of your peculiar looking pipe formation that will cause players to run past without investigating, like a magician using misdirection. I placed a ? block with a powerup and a single goomba. Screenshot 3

4) Make the pipe on the other size of the checkpoint extremely obvious and without any distractions on screen. Screenshot 4 The player will go through it, find themselves back at the beginning, and discover that the peculiar pipe formation at the start was actually a warp pipe that leads to the middle of the level. Screenshot 5

Obviously, once the user learns that the pipe behaves this way they can use it to skip half the level. If they encounter the same design in another level they can likely deduce how it behaves and choose to abuse it. The design can be tweaked to mitigate this, but that's a limitation I'm willing to accept. It's not all that different from using warps in the NES Mario games to skip half the game.