The Jeep I am trading in has always been well maintained and is in good condition as it sets with 60k miles. I have about 4-5k in aftermarket parts in the Jeep and I am hesitant in going through with the deal for the sheer reason you mentioned. I test drove the vehicle and inspected it to the best of my ability, it was bought from auction and has 2 owners. One put 36k on it & the other did the rest. No signs of previous mods that I can tell but it does have an aftermarket shifter so it very well could have been. The dealer said they received no service records as well. They also mentioned a warranty on everything to 100k miles which doesn’t give you much room to play.That entirely depends on the vehicles history and the modification or lack thereof.
As a long time Jeep owner it is worth knowing these are every bit the basket case the Jeep's tend to be. Maintenance is inexpensive and simple but frequent and they have some issues that tend to be common like blown ringlands and spun bearings.