That actually sounds pretty cool. Does that mean, technically, that no one could really ever roll a really bad character?
Theoretically if you rolled, say, a really bad CON and really high DEX, flipping it would just swap where the problem was. Either option would leave you a less-survivable than normal character.
But yeah, in GENERAL, allowing a "flip" means there are no "hopeless characters". Any set of below-average stats can be inverted to become an above-average set. This is one of the things I like about it. You never need to roll a second set if you use this method.
1981 Moldvay and 1983 Mentzer Basic both advise using 3d6 down the line, and that the DM can allow re-rolls if a player rolls a cruddy set, and Mentzer actually gives you a guideline for HOW bad is too bad, but sometimes you wind up needing one or more re-rolled sets. With the "flip" rule no one ever needs to re-roll. Saves time and avoids the DM needing to make difficult judgement calls and look mean or soft.
Of course, if your target is at least one stat of 14 or higher, per the Shadowdark guideline, you could still need a re-roll, if you got an all-average set. If I were using this rule in Shadowdark specifically, I might instead say that if, after rolling 3d6 down the line, NEITHER of your two options (flipped and non-flipped) contains at least one 14, you may raise any one stat of your choice to 14 (
EDIT: Or maybe, you automatically raise your highest stat to 14; you may choose if there's a tie). Average Joe just gets that one little choice bump.