Your question is not correct.
It IS advantageous to flank an enemy, because it gives you better chance to hit. But if your chance to hit is, say, 90%, it does not matter if you are flanking - flanking is already factored in these 90%, and your chance to hit is 90%. There are no "normal ninety percent" and "flanking ninety percent", that would be kind of stupid.
To guarantee a hit, you need to GUARANTEE a hit - i.e. get a one hundred percent chance. I've missed from 98% percent, and this is correct - approximately two shots out of 100 should miss.
The only thing you can do to "game" hit percentages is reload and shoot in a different order. The game remembers random number generator state after save-load, and will always roll same numbers for same actions - but you can switch your shots around to miss with low-damage shot and then hit with a high-damage one.
EDIT: upcoming Enemy Within expansion is promised to have a configurable option of saving random number generator state. I.e. with it off, you would be able to simple reload and take the shot until the outcome becomes "fair" ;-)