I cannot positively confirm or refute whether or not the e-pump can/does adjust fueling on a per cylinder basis. I also have never done an apples to apples comparison e-pump and m-pump on the same engine/same car and don't know anyone who has. Because of that it is quite hard to do a fair comparison. It would be a fun comparison, but I have plenty of other things to do. I think that retarding the timing probably has more to do with idle vibration than per-cylinder fuel quantity adjustment. I have not found the idle vibration to be any sort of issue on any of my mTDIs but different people have different sensitivities. From cold start the idle will creep a little on an mTDI. I've never considered that to be any sort of issue. I am currently running two eTDI ALH Jettas and a '91 ALH mTDI vanagon. I'll go do an apples to oranges comparison on vibration... Ok, I just cold started each of them and the idle vibration is remarkably similar in the driver's seat. Seat-of-my-pants told me the mTDI vanagon has a little less vibration at idle, but the engine is also farther away. There's obviously markedly more vibration that you can feel in the accelerator pedal when under way with the mTDI, because the eTDI pedal has no mechanical connection to the engine.
One thing that I KNOW to be true is that a properly assembled mTDI is intrinsically MORE reliable than a properly assembled eTDI. The mTDI is intrinsically more reliable because it has far fewer potential failure modes and almost none that do not simultaneously exist with the eTDI. As you mentioned the pumps are internally a little different from each other, but I believe they are similarly reliable. Honestly I haven't ever seen a properly built mechanical pump fail (other than leaking) except from bad fuel or from someone messing it up. Aside from the injection pump itself, you have the accelerator cable on the m-TDI vs. pedal potentiometer on the eTDI. It is not unheard of for either one to fail. I think they are similarly reliable. The additional failure modes that the eTDI has that the mTDI does not have, include any of the parts of the electronic engine management, e.g. ECU, crank position, pintle lift, map, clutch pedal switch, brake pedal switch, vss, etc, etc... Each of those parts a quite reliable but any of them can and occasionally do fail. Also, on the eTDI, you are relying on actually having those electrons flowing. If your alternator fails, you have a fairly limited amount of driving possible before you are dead-in-the-water. The mTDI can run for an extended period of time with a 9v battery connected to the stop solenoid or indefinitely with the stop solenoid removed removing the requirement for any electrical system at all. I've heard people say that it is easier to get parts for an eTDI than an mTDI. That idea is utter BS. It is always easier to not need to buy a part because your engine doesn't have that part on it... I have heard people say that the eTDI has OBD so diagnosis is easier. Again, utter BS. The OBD only has the capacity to diagnose the parts of the engine that do not exist on an mTDI. Virtually any failure of an mTDI is just as likely to occur on an eTDI and the eTDI OBD system will not help at the diagnosis.
Both engine management systems are fine. Neither install is overly difficult and provided quality work is done in either case they can be reliable. I have owned both eTDI and mTDI for several years and both are excellent. On stock eTDI vehicles I would not go through the effort of pulling the electronic engine management and installing an m-pump. On a conversion I would not do the extra labor of the electrical install in order to end up with a less reliable vehicle. Honestly, I'm so exhausted with the mTDI vs. eTDI conversation that it's really hard for me to write this type of post.