Actually, this is precisely what Youth Soccer Rankings did not do, and why I like that site so much and wish it had the resources to get current.
It is not a point based ranking system like GotSoccer. Instead it is a form of power ranking that only takes game results into account. It doesn't care whether those results are from a regular season game, or a tournament, or what kind of tournament. It simply looks at the game score and the ranking of the opponent. By having a giant database of recent games, it can look at results between common opponents, and common opponents of opponents, etc, to build a mathematical power ranking that is more accurate than the point based system you mention and which is used by GotSoccer.
The point value assigned to teams by Youth Soccer Rankings is not a reflection of how many tournaments the team entered, or the perceived quality of those tournaments. Instead, the point value assigned to the team is a power ranking value that can be used to predict how two teams will fare head-to-head. Simply subtract the value for the two teams and that predicts by how many goals one team would beat the other.
I discovered it last year and followed it for the teams in our regular season bracket, as well as the tournaments we entered and I was quite surprised and impressed how good its predictive value was.
p.s. I am not associated with the site in any way. I am just a fan who thinks highly of concept and the implementation.