The Institutions should know the rules and not the individual players or parents (for that matter, even the well informed program director). Each school has it's own NCAA Compliance director and nothing happens on any of their properties that is not approved by compliance.
A few years back the NCAA took the skills part of showcases away from D1 campuses. It was still allowed at lower levels and the games could still be played there. So many showcases were run with skills off site and the games on campus.
The entire "MLB Scout Team" is fairly new the last few years and I'm sure the NCAA will sooner or later address their concerns with them. On your final elegibilty questions from the NCAA there are questions regarding who you played for, whether your paid or played for free etc etc.
The 2 factions, MLB and NCAA are on different sides of the table and it's only a matter of time. As far as I know, travel teams can and have been playing on college campuses. If there is an issue with "Scout Teams", I am unaware and unfamiliar.