Take GT racing then - SuperGT as a good example.
They run the same length races as F1 (300km give or take) on the same sort of tracks (Suzuka, Fuji) with the same approximate grid size (well... sorta - just over 30 in SuperGT, just under 30 in F1).
Now let's take last year's SuperGT qualifying times.
Suzuka 300
GT500 Pole - 1'53.182
107% - 2'01.105
GT500 last starter - 1'55.019
GT300 Pole - 2'05.391
GT300 last starter - 2'11.887
Now, let's be kind and change the 107% rule from time to speed - the point of it is, after all, to avoid dangerous speed differences. Vettel's Pole at Australia of 1'23.529 equates to an average speed of 142.01mph. 107% slower would be 132.72mph - a phenomenally dangerous average closing speed of 9.28mph (less in tight bends, more on fast ones).
Apply this to the above SuperGT example. The HSV010 pole lap of 1'53.182 equates to an average speed of 114.79mph. The slowest qualifier that actually took part in the same race managed an average speed of 98.51mph - for an apparently safe average closing speed of 16.28mph. Not only is this a higher closing speed than in F1 - on the same track over the same distance - it's also a much more significant proportion of the cars' performance. But safe for SuperGT, apparently.
It rather seems that the 107% rule has little to do with safety - any racing driver worth his salt should be able to drive around a car that's only 7% slower than him, especially if he's come through lower formulae first.
But then again, the blue flag rule is different in F1 compared to other motorsports. In F1 it means "get out of the way or else". In other motorsports it's just a warning of faster cars approaching from behind.
Other cars are part of racing. Having to find your way past a car that has a race pace slower than yours is part of racecraft. Otherwise we may as well just return to the qualifying format of a few years ago (each car gets an outlap and an unobstructed flying lap), call the results there and move on to the next event.