Hey Chris,
I think your problem is that you don't get what an "Outer" and an "Inner" mystery are. Ars Magica is pretty confusing sometimes, but when you sort through it, there's a pretty clear structure.
The "Outer" Mystery is the single root mystery which every Cult member has in common.
An "Inner" Mystery is anything else.
A "Unique Inner Mystery" is one of the four Mysteries which are conferred when you join a Confraternity.
In the case of Verditus, reread the chapter carefully. You're missing some crucial words in key places.
But here's a breakdown of how the Mysteries are arranged, and how a magus navigates through them.
1.) Joining House Verditus: The Outer Mystery.
There is only one. The Outer Mystery grants the Minor Hermetic Virtue: Verditus Magic. It is either gained when Arts are opened, or by a ceremony and training culmunating in the Embrace of Boethius
2.) Make the decision to join a Confraternity, or not.
If yes: Confraternity immediately initates a Minor Mystery, giving a Minor Virtue. Only Confraternity members can initiate these Mysteries in this way.
If no: Procede to step 3.
3.) House-wide Inner Mysteries.
If a Confraternity member: Initiate these Mysteries according to the "road map" of the Confraternity.
If not a member: Initiate any of these mysteries so long as you A.) Can find a mystagogue and B.) Have sufficient Lore. (i.e., 5 for major virtues.) You may initiate them in any order, mixing Major and Minor as you see fit, though minor mysteries are easier and require less of a sacrifice.
That's the whole thing.
Life would be easier if the publishers would use tables. But I've read Verditus probably more than is healthy.
Verditus has by far the most relaxed path through mysteries. Enjoy it! It makes characters very easily customisable.