Makes sense. I also figured the two were the same, judging from your response they are not. To the internet to find out the difference!
Any other cons of a supercharger for a TJ the OP should be aware of?
Bolt on? Just make sure the engine is sound before you add forced air induction. Good valve train, reasonably equal compression, transmission and transfer case up to snuff, etc. If you have issues in your ignition system, forced air induction will show that up in short order. The oiling system for superchargers and turbos need to be absolutely reliable and bullet proof to make them live a long and healthy life. An intercooler is worth the time and effort as it will decrease the chances of detonation or preignition. You're going to probably want to run premium fuel. Oh, make sure the rev limiter works and is set correctly. A blown drive line part or missed shift can have drastic consequences with a forced air induction system.
Superchargers will increase torque and horsepower from just off idle with no lag to speak of. Turbo's are getting to be the same way, but they have to be sized correctly on the turbine side and on the compressor side.
Full on custom? There's a lot to consider. Compression ratio, combustion chamber volume / matching, piston cooling, ring configuration, valve setup, cam profile, crank and rod modifications, exhaust mods, intercoolers, water / alcohol injection, fuel supply and injection, vacuum operated accessory modifications, head gasket design and mods... I built a blown, injected Mouse motor back in the late '70's. It was a thing of beauty and produced awesome power. What I should have done, upon reflection, is just plugged in a crate Rat motor and been done with it. There is no substitute for cubic inches in the pursuit of performance. A super/turbocharger just makes your engine think it's larger than it really is. That's the bottom line.