Something to note about the Baseball America Top 100: The Astros are lightyears ahead of some other organizations in terms of international scouting. They've signed and developed numerous guys who were basically unknown to Baseball America and other similar websites. Think Javier, Framber, Urquidy, Blanco. Yordan Alvarez was under the radar as well and the Astros played a big role in developing him.
Baseball America and other similar websites don't have the time or resources to scout these international guys.
There's similar guys in the organization now. Luis Baez, Kenni Gomez, numerous others.
At the same time, the Astros farm system lacks star potential at the top. Especially AAA. You have Drew Gilbert in AA but he's still getting adjusted to that level. Ryan Clifford also has superstar potential but he's a good ways away as well.
This is ultimately why Jim Crane hired Dana Brown. Crane likes a lot of things about Brown but the main reason was his ability to scout and draft. The farm system needs replenishing, especially after not having a first or second round pick for a couple years.
So, yes, these rankings certainly don't tell the whole story. But they also paint a bigger picture of where the farm system stands as a whole.