Having 3" of suspension lift is about the max you can go on a TJ without having serious driveline vibration issues that require a lot of expensive (or inexpensive but less desirable) modifications. The proper way (that also costs around $600) is to install a slip yoke eliminator (SYE) kit and then get a custom made double Cardan (DC or, more commonly but incorrectly CV) driveshaft. This fixes driveline angle issues from lifting. The more common, less expensive ways are either the much hated transfer case drop or the less hated body lift with a motor mount lift.
A 1.25" body lift is not going to hurt anything. The argument is against the boneheads who "lift" via only a body lift, like 3" of BL or more, which is very unsafe.
The Zone kit is not the dimensions you listed, but actually a 3" suspension lift with a 1.25" body lift and a 1" motor mount lift. This gets you the 3" of suspension lift and then removes any possibility of driveline vibes with the addition of the BL/MML. It is a poor man's way to get the higher amount of lift with no TC drop and no driveline destroying vibrations.
It is not a great lift by any means, but it is an excellent package for such a low cost. It gets you up and running so that you can roll on 33" tires with all the clearance you need, decent flex, a fair ride quality, and like any kit, if you dislike certain components you can swap them out once all the main work of installing stuff is concluded and you have ridden on it for some miles.
The option of adding a JKS adjustable front track bar is worth the cost, and several other good options are available, like the much hated cam bolts to fix angles in the control arms by allowing you to alter certain lengths without purchasing control arms.
If you go this route, like mentioned above, you can get the basic lift and some tires for about $1500, which is a good price for all that.
A 4" straight up suspension lift will require lots of alterations that the Zone kit does not have, or that the Zone kit sort of rednecks its way through. The compromises are, to many here, more of a negative than those of the Combo kit.
It is apples and oranges, but the Combo kit is much more popular for a reason.
Many here have 4" of lift with zero BL, but that costs a lot of money to do right. My lift cost me about $3500 overall. I am a lot older than many of these guys, so I can afford that. If you are young and do not have a good paying job the Zone is an excellent choice. And for some who are just frugal and do not daily drive their Jeep all that much (meaning that they have another vehicle) it is still "good enough" for off road duty with some highway miles thrown in there.
I will be doing a 1" BL at some point. I will add in a 1" MML. This will allow me to do a tummy tuck and perhaps get my gas tank up a bit higher, too. Further, the upper, rear shock bolts become much more accessible with a 1" BL. Mine were rusted in so badly that I want to have easier access to the tops of them for any future shocks installs I do.