Your question is not a very valid one, because you imply that a Footlocker champ should be the top-American at least at NCAA's when they get there. There are a lot of factors that make this not a valid premise.
Without listing the reasons, let's look at this brief 25 year Honor Roll and see how they turned out
BOYS
2002 Chris Solinsky - top frosh this year, outstanding so far
2001 Timothy Moore - solid college career so far
2000 Dathan Ritzenhein - On his way to the best record in XC since Pre and Lindgren
1999 Dathan Ritzenhein - see above
1998 Jorge Torres - ~54, 3, 2, 1 - says it all
1997 Abdirizak Mohamud - he won during a down period, but I don't think he has put his best effort into running in a long time.
1996 Abdirizak Mohamud
1995 Abdul Alzindani - Ran at NC State I believe, solid results. Don't know if he ever did anything worthy of a FL winner, but he did run in NCAA's.
1994 Matt Downin - XC stud at Wisco. I think he was top-5 twice and top American once.
1993 Adam Goucher - 2nd as a frosh. 1st as a senior.
1992 Brendan Heffernan - I have no idea.
1991
Corey Ihmels - I have no idea. Anyone?
1990
Louis Quintana - dominated in HS. Don't know many stats from college. He did run 13:53 in college and have some good results, but it even surprised him when he didn't have the same type of success in college.
1989
Bryan Dameworth - I don't know. Anyone?
1988
Brian Grosso - Grosso was amazing in HS. Ran a bunch of sub-9:00 3200's at a time when this was rare and had been rare since Scott Fry and Eric Reynolds. Many stories about this cat. I have one from a recruiting trip. I don't know how well he represented in college. I believe he went to Arizona with Davis. Anyone? Anyone? Bueller?
1987
Bob Kennedy - don't need to say it.
1986
Marc Davis - stud in college. Ran a 13:32 as a sophomore and was No. 9 collegian all time. Steeple champ too.
1985
Reuben Reina - stud at Ark. He may have made it to top US guy at NCAA if he didn't run on the same team at the same time as Falcon.
1984
Scott Fry - stud at Wisco. Was on two National Champ teams at Wicco. i don't know what he did individually. He ran at least 13:49 at 5k.
1983
Matt Giusto - 3rd in 1986 NCAA XC. 1st in 1988 5000m. Multi-time National Champ at 5k after college.
1982
Eric Reynolds - Never made the impact in college that he did in HS. Attended UCLA.
1981
Charles Alexander - i have no idea.
1980
Jay Marden - I think he went 28:00 as an open runner in 1988. Don't know what he did in college. Before my time.
1979
Brent Steiner - KU? Anyone?
>>>>>>>>>>>>>>>>>>
So there you have it. There are about 14 out of 22 unquestionable success stories post-HS. And several flops, for many different reasons. Several of them I don't have info on, and they may have had strong college careers too, i don't know.
But it is wrong to say that only Ritz, Torres and Goucher lived up to expectations.