It is not true that they do not score points for their team.
Lets say the varsity guy and the JV (Unattached guy) from the same team place 1st and 2nd place at the tournament in the same weight - it prevents another team from scoring those points in that weight.
When I set up a tournament with PES software I utilize Team X (or another variation) for quality high school team affiliated non varsity wrestlers who are added to fill in a bracket. The Team X participants may or may not be allowed to score team points for TEAM X, not their respective high school.
If in the case you mention, the unattached wrestler placed higher than an opposing wrestler - what is the problem? The opposition will have to improve in order to beat the opposing teams non varsity wrestler.