Interesting thread. There are at least 2 factors here. A brand new, fully functioning (clean) turbo has some turbo lag, but it is not that bad. With a tuner or chip, it is even more acceptable. However, there will always be some lag.
I don't think the lag is there to protect the drive train. If it can take 500 ft pounds out at 2500 RPM's, it can take 300 ft pounds at 12-1500. The lag is there because that is what 7-8000 pound vehicles do with a motor like this. And in all honesty, for the large majority of people who own them (who use them for general towing, etc.), the lag is not an issue, they did not buy a race vehicle. If you have been around through the 70's, 80's, 90's a nd now, you would consider the 6.0 a real top performer (again, as a tower, work truck, not as a race vehicle).
The other thought was that the lag was there to help with emissions. That, I can believe. That is, I know they have taken several steps to reduce emissions, most notably, the EGR system as well as the fueling strategy (which leads to some lag). So, yes, with a tuner or chip, you should get that back. With a properly running turbo, the lag is not that big a deal.
Now, the lag you talk about. I know it, all too well. And I know what the problem is. And a tuner or chip really won't help. These engines have an EGR system that basically recycles exhaust gas at lower RPM's. That acts as a double whammy against performance. 1st, it sends spent air (no oxygen, just basically nitrogen and exhaust fumes) back into the combustion chamber. This helps in reducing NOx emmissions, but just crushes performance. So, your turbo, which needs all the exhaust gas it can get at low RPM, is being robbed a little. That is, when you recycle exhaust gases, you can't combust as much of the incoming fuel, so you generate less gas phase molecules, which are the impetus for spinning that turbine. Another factor related to these recycles gases is, that they are inevitably hotter than the ambient air, so this is yet another negative.
The 2nd issue with EGR's is that on this truck, they work well for about a mile. After that, soot starts to coat the valve, which then makes it work poorly. It doesn't close all the way when it is supposed to, or in some cases, gets stuck open. It is a total POS in terms of its design. I understand what it is intended to do, but there is no question among those who have studied it, that it fails, miserably, at doing its job mile over mile. Another additional problem with it is that the soot it promotes also coats your turbo. Then the vanes don't respond well, and that, more than anything, just kills response.
What you are feeling is this last item, I guarantee it. Your turbo is not running right, and it is most likely due to the EGR enhancing the soot exposure to the turbo. No tuner will fix it. The best option is to get it cleaned (or clean it yourself). I bet you will be amazed at how gummed up those vanes are. Turbo maintenance is almost never discussed, but it is critical to the performance of these trucks. I think that the turbo should be cleaned every 10K or so. But no one really does.
ps1: there is a fix for the EGR, but you will have to PM me for that.
ps2: on back-pressure; the less, the better. These are not gassers. Your turbo runs most efficiently if the pressure on the feed side is as high as possible (exhaust flow) and the exit side is as low as possible. Hell, a vacuum on the exit side would be even better. The blades of the turbine accelerate or spin acording to a complicated formula that is proportional to the pressure drop across it. That is, if Pi is the inlest pressure (exhaust gas feeding the turbo) and Pe is the pressure of the gases as they exit the turbo and enter the exhaust pipe, then you want Pi-Pe to be as big as possible. The bigger it is, the faster it spins. The faster it spins, the more boost it makes.