Unless I misunderstand the original post, you want to buy two tickets on the same flight, one with each FF program, and get credit for both when you fly.

Since you only board once and therefore they only collect one boarding pass from you, wouldn't the other one be recorded as a "no show" and earn no credit?

You could always say you booked the second seat for comfort, for your cello, or whatever, and check in with both. Might work that way. I doubt a gate agent or electronic boarding pass reader would care if the FF numbers on the two BPs are different.

In that case, to answer the original question: if a flight is worth it as a mileage run for one program, it should be even more worth it with two programs, since the ancillary costs such as airport parking or travel and meals en route don't go up. However, this presumes that (a) you value the miles in both programs about the same, which would not be the case for many people here who value miles in their primary programs much more than any others, and (b) flight-related bonuses, which often justify a MR through double miles and so on, are good enough in the secondary program to justify the cost of the second ticket.