I would say you really have to evaluate it on a per-rune basis as some of the scaling runes surpass their counterparts earlier. For example, the progressive +armour runes catch up at I believe level 9, while most of the others I checked didn't catch up until ~level 11-13. Also some heroes may benefit/require an earlier advantage while others are already quite dominant at the start of the game, so having the greater benefit after level 9, 11, 13, or whatever it is may be better for them.
Though there is another deciding factor which can't be ignored and that is the infamous level 1 team fight, in which flat runes and starting items play a huge role. Team fights this early happen almost never in low-mid Elo games and even in high Elo games they often don't happen. So you have to decide if you think a greater chance at winning the potentially very early first team fight is worth sacrificing greater mid-late game potential. Also who knows, your early-game runes may save you from an early FB attempt by 3 heroes, shaco etc while your scaling runes would be practically useless.
With all that said, and taking in to consideration that the current meta-game more often favors those that succeed early the flat runes tend to be the popular choice, but I wouldn't discredit scaling runes entirely and for some attributes it may be your best bet.
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