The OP has a very good point, and probably a valid complaint...but the difference is nowhere near 5 seconds. Here are some of the relevant sections from the NCAA rulebook, which should be required reading for everyone posting on this thread:
http://www.ncaapublications.com/Uploads/PDF/mw_trackandfield_rulese88cb2a4-3dac-4a6d-b6c2-c0fe5a66ffe7.pdf
"The track may be bordered on the inside by a curb of suitable material approximately 5 centimeters in height and a minimum of 5 centimeters in width. The edges of the curb shall be rounded. See Figure 1. If a section of the curb must be temporarily removed for any reason, its place shall be marked by a white line 5 centimeters in width and by cones at least 15 centimeters in height. The cones shall be placed on the track so that the outward face of the cone coincides with the edge of the white line closest to the track. The cones shall be placed at distances not exceeding 4 meters."
"Measuring Distances
ARTICLE 5. The distance to be run in any race shall be measured from start to finish between two theoretical hairlines. Lane one, and all distances not run in lanes, shall be measured 30 centimeters outward from the inner edge of the track if a regulation curb is in place. If a curb is not used, lane one shall be measured 20 centimeters from the left-hand lane line. For world, American and NCAA meet records, and championships qualifying, a regulation curb or cones must be in place. In races run on straightaway courses, the distance shall be measured in a straight line from the starting line to the finish line. For all races in lanes around one or more curves, the distance to be run in each lane, except lane one, shall be measured 20 centimeters from the outer edge of the lane line that is on the runner's left. Lane one is to be measured as stated above."
Indoor Track:
"Where the inside edge of the track is bordered by a white line, it shall be marked additionally with cones. The cones shall be at least 15 centimeters high. Cones shall be placed on the track so that the outward face of the cone coincides with the edge of the white line closest to the track when the track is surveyed based on the existence of a curb. Otherwise, cones shall be placed on the infield adjacent to the line. The cones shall be placed at distances not exceeding 2 meters on the curves and 10 meters on the straightaway."
Now for my analysis--the rules make it clear that any track used in championships qualifying has to have a curb, so the Notre Dame track must have been "surveyed based on the existence of a curb." When the track doesn't have a curb, cones on the outside of the lane line are just as good--so if the cones had been in the correct location there wouldn't be an issue (though it's pretty bogus to not put out the curb for such a high level meet). From the Flotrack video it looks like the cones were on the inside edge of the lane line, which is where they would be for a track surveyed without a curb. This means a 10 cm difference in the track's official radius, or a 20 cm difference in the track diameter. On a 320 meter track, that's about 63 cm per lap, and 785 cm for a 4000 meter race. A 9:30 DMR team averages 7.02 m/s and would take 1.12 seconds to cover that 785 cm. 13 out of those 15 teams would still have auto-qualified.
According to a strict interpretation of the rules, the misplacement of the cones means all races on that day are useless for qualifying. However, since the race is documented on video and not controversial (besides the track length issue), the fairest treatment of the athletes involved is to allow marks from the meet, but apply a conversion based on track length.