Bringing back the strikeout now for the moment. Effectively, infield popouts and strikeouts are equal. Neither has a chance of advancing runners and neither results in double plays. Based on above, a Strikeout is worse than a deep flyout to right.
A fly ball does result in two outs when guys tag up and get tossed out. Its infrequent, but it does happen.
A fly ball leading off an inning is no better than a stikeout, and neither is one for the 3rd out. Most players get out 65%+ of the time, so 65%+ of the time the second batter in the inning would not even have a chance of advancing a runner with a fly ball.
You are talking about only a small portion of possible outs, and the probability that a runner is on, has some speed, and a fly ball is deep enough to move him up doesn't happen a significant amount of the time, even if all the outs where long fly balls. Given that they are not all long fly-balls, its even less significant.