I do get that argument, but given how time gaps are calculated in the race itself, that 0.48 seconds would probably get lost in the noise if you checked all the actual timegaps where Carthy tailed in near the back of a group at ST, or allowed for rounding off of Roglic's deficits on Formigal and Angliru. I just feel that it's a random application of the timing to only score TT stages that way, but not gaps on MTFs.It is a timed race: these are times. Carthy was .37 seconds away from being on a time 1 second less; Roglic would have had to have been .48 seconds quicker for the same benefit.
But it is exceedingly unlikely to be brought into effect. Someone will be along, no doubt, to say what the biggest result (rather than simply determining skinsuit colour in a timetrial) that has been thus determined has been.
When there is no TT (or, I suppose, if fractions of a TT second are the same) then it is total of finishing places, not Green Jersey points (so the difference between 30th and 80th in a large bunch finish is potentially very relevant.)