Ah, ok. So you're simply mistaken. While some tuners do that, they don't all do that. I imagine "smoke" tunes probably do. Fortunately the fad of rolling coal seems to have mostly died. Some of the things some tuners do: raise the injection pressure to get more fuel in more quickly, advance the injection timing, remove the fueling delay so the turbo spools up more quickly, raise the boost limit, raise the RPM cut off, raise the EGT limit, change shift points, change the shift pressure for tighter engagement, alter/disable EGR function.....
In many cases a tuner can extend engine and transmission life. If one decides to tune his engine into a top fuel dragster then it's probably gonna be short lived. The problem with tuners is similar to that of nitrous, once you buy the package you can go from mild to wild for 0$. Motors blow up and the device gets the blame instead of the person who got greedy.
I've got at least 600 miles of driving my buddy's 7.3 at different tune levels and many thousand miles driving stockers. The biggest impact is the removal of the power delay when you first step on it. The factory tune keeps the air/fuel ratio lean & clean so when you step on it it adds a little fuel and waits for the turbo to give it air, and the two slowly come up together. The tune lets it fuel quickly to make power right away, which of course spools the turbo more quickly. In stock form there's a slow build up of power when you step on the pedal, when tuned it acts more like a gasser where it responds instantly to pedal input. Less of an issue with later model diesels having multi turbos/variable vane turbos, but they still do the clean burn thing so there's still a delay in response. This brief rich condition is bad for emissions but does no real harm to the motor. Generally speaking, if a diesel ain't smoking there's little chance of it being damaged by over fueling/late fueling.
If I had an electronic diesel I'd research the shit out of which tuner is best for my vehicle and get that one. I would then monitor everything to make sure it's not doing something retarded. A buddy has a Diablo on his 6.4 and I'm sure it's going to kill the thing. He loves the power and the fact that it no longer regens, which also "proves" to him that the engine is running better and going to last longer. It's common knowledge that regen puts fuel into the oil and is what kills a 6.4 The amount of fuel in his oil proves to me that it's going to die sooner than it should. When I told him he had over a gallon of fuel in his oil, which it wasn't doing when it was stock, he said "but it doesn't regen any more". Because it doesn't regen his brain is stuck on 'it can't have fuel dilution' even tho I showed him. When I did his oil change it was at least a gallon over-filled and he hadn't added any oil. It's about due for another change, I pulled the stick last week and it's over full again with 0 added. I can't tell exactly how far over it is because the fuel/oil blend doesn't stick to the stick. If I were letting him run the factory OCI it would probably be dead already. Ford recommends 10k, I'm doing them at 5K.