Blades I have been trying to explain this to you for the past two pages,
2 projectiles of the same weight and speed WILL have different trajectories when comparing xbow bolt to arrows because of
1. length of projectile (the big one)
2. Diameter (wind resistance)
3. surface area of projectile
4. length of fletch
5. height of fletch
and more but feel free to google it yourself!

You hit consistently with your bow because you use the same weight arrow, same length, same fletch, same point, etc every time!!!

So to answer your question physics do change with what bow is used. Even when comparing different compound bows!