And you can certainly make that argument in the context of a man who approached every stage, every day in a yellow jersey, and every climb as a separate goal. One wonders how many TdFs the Cannibal could have won had he decided to ride more conservatively on a daily basis and to make the GC a larger priority.
On the other hand, what made Merckx great was his furious passion for winning everything. Putting limits on that kind of ambition might well have affected his overall psyche. Armstrong is a different kind of personality, much more shrewd and calculating. He set his sights on the TdF GC as his raison d'etre, and that alone became his motivation. Both men were wildly successful, and as I said, you can make a case that Merckx, because of his 5 wins, multicolored jersey titles, and his stage win / days-in-yellow records, is the "greatest TdF rider in history". And certainly you can give him some deference because of the strange incident which likely cost him a 6th title.
But from another perspective, the TdF GC is the ultimate accomplishment in the greatest race. Stage wins, etc., may accent the achievement, but they do not rise to the same level. When people debate the merits of the great riders of the event, the first criterion is always the GC. That is not the only criterion, certainly, which is, I think, your point to begin with. But from my viewpoint, it's tough to argue that the greatest rider in a particular event is not the only man who won it seven (or even six) times, consecutively.
I think it's also fair to say that, in the event itself, he may be the luckiest ******* ever to have competed. Sure, he's had his mishaps with shopping bags and German fans spitting into his face, but for some reason every time he was placed in a precarious situation he managed to escape without a broken collarbone or femur. When Beloki went down in front of him on that descent, it was on one of the few stretches of winding road where Armstrong had a field to ride through rather than a cliff to dive off of. They say a man makes his own luck. In Armstrong's case, I think it's a bit of both.