I am not sure if you are aware of this BUT we are comparing an engine with a turbo to one without one not hypothetical examples of adding a turbo etc etc. But if you want to go that way I will.
Of course engine weight has significance as by having a 1.8t there is a roughly 75 pound saving on weight making the car less nose heavy. This is particularly important in the fwd VW platform- the real world application of the two engines.
Dollar to dollar it is clear that moderate gains are more readily made with the 1.8t which is already boosted. A chip can make gains unachievable by a vr without expensive addition of a turbo or supercharger.
As far as high dollar tuning I would guess the cost to build would be similar since more valves etc on a 1.8t but more $ for 6 pistons, rods. As for the strength of factory bottom ends it depends on which 1.8t, but here is 490WHP on stock bottom end AEB:
http://forums.vwvortex.com/showthread.php?1915946/page1
It is pretty clear that the 1.8t is superior to a 12v vr6 in terms of value (mid-level), performance (75 pounds lighter) and efficiency (same power out of less displacement). As I said before that doesn't mean it is "better" to
you since you could like some qualitative aspects of it. However, it is quantitatively superior.