The only required use of the Bait Bag is in Bird's Peak Rock, where you are supposed to use a hyoi pear in order to trigger the switches to unlock the door leading to a triforce chart. It is possible to trigger all switches using bow snipes except the highest one and as such, it isn't possible to skip the bait bag in a bug limit speedrun.
Go to Bird's Peak Rock (quadrant G5). Position yourself to the far left of the grated passage way, on the pictured texture, and pull out the grappling hook. Aim it into the cliff until you see the targeting icon appear. Grapple to the post, and as you begin swinging back towards the cliff, immediately let go to clip through the gate.
Get chest storage and bomb boost up the ledge on BPR. With chest storage you can sidewalk past the gate and enter the loading zone early.