The SEs are below the sport and limited. I think 4-cylinders only came in the SE trim. No power mirrors, locks, rear wiper, rear defrost; earlier models might not have gotten the center console. Most of my 2dr 2wd 5-speed 4.0s were SEs.
That's just the marketing department. They can't call something "base model" or anything usefully truthful. Gotta put cool numbers and letters on the name.
It's kind of like getting a snow report from a ski resort. If they've had clear weather for two week, it's listed as "four to six inches of fresh powder", and if the slope conditions are "great", that means it's June.
SEs could come equipped with power equipment, but you had to get them as options and usually more expensive than power equipment that comes with a package such as limited, classic or sport. We bought a brand new '92 XJ SE that was a 2 door, 4 cyl, 5-speed, 4x2 and manual everything. It was just over $13k with the Chrysler "green slip" discount, and I loved that little Jeep.
I suspect that even the SE had something installed beyond the base, because at least through 95, there was a true base model with no designation at all. My no-model 95 has a few options (carpets, rear defrost and wiper, remote mirrors, roof rack), but came with no gauges, no power anything, minimal interior lights, etc. As far as I know what options it has were chosen individually.