Some you get your value back, the ones you mentioned are definitely on that list. Some are game specific, an example is Tron's wire kit or Creech Mike D mod you will get your money back on. Pinsound board will get you your money as well, expensive mods that feel like a must.
Other mods like cliffys, Titan rubbers, little toys etc you don't really get back on. You often lose some money on armor, powder coat. It's very game to game and specific to how much the machine is truly enhanced.