while generally true, i'm not exactly agreeing with you all on the finer points.
as far as i know, both the vvti and non-vvti have the same oem exhaust manifolds. they are not tuned or anything fancy, just straight tubes with exhaust ports each each cylinder like typical stock manifolds. going to headers on an 04 non-vvti motor removes a major restriction to produce more power as opposed to keeping the restrictive exhaust on the 05 vvti motor which makes more power by changing the valve timing. you can argue it's the same effect, but so far no one has develped a dyno-proven header design that works at all rpms with the vvti motor so you simply cannot tune it to run well at both low and high rpms by changing the exhaust. to me, adding the headers is the simplified, elegant way of solving the problem at all rpm levels as opposed to the more complicated vvti solution.
another finer point has to do with rear end ratios and towing. yes, you can do a lot with tire and wheel selection. i personally like the 4.10 gearing and would even consider going higher on my 04 DC. i'll probably do this with smaller tires this fall. for me and what i tow and the hilly conditions i drive in, this is a very good gearing for me. i don't know about the 3.90 gears in the newer trucks and how that works out with the 5 speed tranny and overdrive, but it seems intuitively that this is going the wrong way for towing - especially if you want to run larger tires. either way, it's possible to get higher gears for either truck. with the non-vvti, you are more likely to want to do this mod even with the more powerful engine, so you can get into the "sweet spot" for your towing conditions and load.
as far as major mods go, there are more for the non-vvti (supercharger, chips, header options, etc.) whether you need them or want to do them on a vvti or non-vvti is a personal choice. i think either engine, being a smaller block design with 32 valves is going to run better at higher rpms when towing a large or heavy load. if you want low end torque, you'll have to supercharge. that is the only option with the 4.7 and is only available for non-vvti motors. or, buy an 07 with the larger displacement engine.
one other last point on the two engines. the non-vvti is a proven design that has been out since 1996. the vvti engine has not shown any problems yet but has only been out for two years. the inherent additional complexity of the variable valve design has not been proven in this engine block over the long haul. only time will tell as owners go up and over the 100,000 and 200,000 miles marks in statistically significant numbers.
both are fine trucks and fine engines. i think it comes down to personal preference and needs and there aren't any significant advantages over either design for the average user unless you get into specific towning scenarios or terrain.