The MD80 uses about 200 kilo's of fuel for a 10 minute taxi and takeoff. Given they used 10 minutes out, 10 minutes back and 10 out again means they used let's say 600 - 800 kilo's. But remember, they are lighter, not heavier, so that fact should have helped their case, not hurt it. They would have theoretically taken off with more speed than needed. But with these weights it would not have differed more than 2 knots. I don't know if they refueled, I asked recently about the time spent at the gate for another reason also but don't know yet. If they refueled you would have the correct speeds again in the FMC. If they overfueled you would come back to the same 2-5 knots at the most per ton of difference. our MD's don't have intergrated FMC's as we don't have EFIS. But I think the speeds are manually entered in EFIS MD's. Not sure though.
In a recent post I talked about the commands "Flaps up" and "Slats in" given by the captain while arriving at the gate. Our operation does it independantly of the taxi in checklist although it is also stated in there.
They are done last minute to reduce FOD while taxiing by keeping the flaps at 15°. If they decided that it would be a quick fix and omitted all checklists so they would be ready to go when finished it could be one scenario of having the high lift devices not in the correct position. I say this because if they did the checklists it is very difficult to miss this item. It is many times the first one on the taxi out.
One last thing. I remember someone posting about the fact that he's never seen an SOP where the F/O executes an abort. In our operation, the F/O handles the full takeoff, including a possible RTO. The only limitation we have is if a F/O gives a "stop" command it should be regarded as an advice to the captain. Otherwise the first officer handles everything and also keeps his hands on the throttles until V1....
. I know however that indeed there are many other companies where this is not the case.