For domestic US travel, $0.02/mile is almost always a bad deal if you can buy any kind of discounted ticket ahead of time. On most airlines it is 25,000 miles for a free roundtrip. That's $500 if you value the miles at 2 cents each. In the example you site, the ticket in question could be purchased for $400, obviously a better deal. You are correct in noting that the purchased ticket would also provide you miles, 5000 in this case, not including any bonuses. Therefore, you could consider the true award cost to be 30,000 miles (25,000 for the award ticket plus the 5000 "opportunity" miles you are giving up because you are riding free). This suggests that at $0.02/mile you are really paying $600 for that award ticket. Purchasing the ticket outright is, of course, still a better deal than using miles.

I find the $0.02/mile valuation high (again, for domestic travel - don't know much about international). My reasoning is that if you can buy them for 2 cents each from the airlines their real value must be lower than that. I usually value them around 1.5 cents each.