Couple of comments, if I may ...
If you look at the inboard side of most high-bypass engine inlets ..
I had thought that these were for a more general high alpha stall margin concern with larger engines ? Chines - another example of VGs in action - are associated with reduced nacelle-wing clearance and resultant shed vortex flow over the wing (rather than under as with the smaller diameter low bypass and straight jet engines of a bygone era).
See, for instance, -
(a)
http://www.smartcockpit.com/aircraft...enerators.html
(b)
http://www.icas.org/ICAS_ARCHIVE/ICA...PAPERS/542.PDF
(c) (having trouble linking to this paper - google Thierry Sibilli PhD thesis and Cranfield ) ... pp 155-177.
The theory can get a tad heavy but the pictures are great ... even slower chaps such as I can get the gist of what's going on ...
I recall, years ago during the early 733 days in Australia, a CASA airworthiness engineer asking me over coffee whether I would be concerned taking a 733 minus a chine without any engineering consideration. I think my ashen face gave him my answer ... it transpired that a local operator (the other one - not mine) had done just this a few days prior ... CASA had, quite appropriately, taken a dim view of the matter ...
the FCTM wording specifically calls out "during flap retraction"
Perhaps the OEM emphasises flap retraction as that is when the margins routinely are likely to be reduced. I recall, during a period working for an operator with 744s, that the problem was a routine crew concern for high weight departures.