Surely you aren't comparing Allen's comp. % in the pros to Milton's in college football. For one, there is little difference in their respective numbers, but Allen is throwing against pros in much tighter windows. It's fine to compare their physical skills, but Milton isn't in the same zip code as Allen as a passer.
Allen has the strongest arm in the NFL, currently. Joe's may be stronger, but its negligible at that point. Allen can throw it 80 yds, so how often will it really be practical/relevant that Milton can maybe throw it 90 yds? It's probably sufficient to say that both have strong arms and can make every throw on the field based solely on arm strength.
What evidence is there that Milton is a better runner? Milton has rushed for 627 yards in 40 career college games. Josh Allen ran for 762 yds in 16 games last season, alone. In college, he ran for 767 yds in 27 career games. Allen ran a 4.75 40 at the NFL Combine and Milton ran a 4.78 40 at Tennessee's Pro Day, last spring.
There is certainly a place for Milton in the NFL based solely on his physical traits. Someone is going to fall in love with his ability and think they can be the one to refine him much like Heupel has twice, now.