Well there is one flaw in your theory and that is that
The Concorde fleet is grounded bwahahahaha I just defied physics 
. lol j/k
Seriously though I definately understand the whole atomic clock deal I'm just sayin' lord knows what else might effect this thing other then "time dialation" yah know? At least as we think of it. Not saying your wrong obviously but that whole "time and space" area of science is as you said best avoided for the sake of human sanity and health lol
Well good thing about the "FTL" in my story (even when and if I can get good enough to write a book, all I'd need is an editor like most authors
) is that it's "warp points" (name to change trust me) which are actual "folds" in space which don't actually make you go FTL so much as temporarily exist in two places at once and then fully "materialize" in the new place. Unfortunately this has rather bad effects on human orientation leaving earlier generations with "jump shock". Though as stated with my newer chapters the newer generations of GFGs are better able to compensate for this and thus little to no jump shock.