Charlton is a "guide" for the casual collector. Some of the questions that you ask go much more in depth than Charlton has room to publish every year or that they, themselves, have the copyright authority to put in their books. From the questions you ask, I would recommend you buy a copy of Rob Turner's "Dies and Diadems" that will answer all your quandries.... it's somewhat costly but a must-have book when you want to get into the weeds with Victoria Large Cents.
Believe it or not, the specimen 1876 coinages (the first out) were actually Obverse 1a's, with the rounded neck truncation further away from the bead. The 1876's for circulation wwere Obv 1's, with the pointed, almost-at-the-bead neck truncation. There are also differences in the angle of the sweep back up from the truncation toward the back of the neck, the general angle that the base of the back of the neck makes as it rises to the back of the head, and the intersection of the crown tip with the bead. Charlton shows the neck/chin and lip photos, but they are not markers for the differences between a 1 & 1a and shouldn't even be there. The Obv 1 & 1a portraits are physically different images and, as such, are major varieties .. there are 2 different masters.
There are more than a couple intermediate steps in the hierarchy between the initial master and the working die. At any one of these steps, something can make one component different from its brother ... broken/cracked relief elements, plugged incuse elements, hand-correction of mechanically caused faults, etc. Call them what you want wherever the difference appeared (hub, matrix, punch, master), but the relief punching that forms a working die is done with multiple strikes/impressions on the die, with periods of annealing and hardening between the strikes.... not necessarily done on the same day or week. When the punches are placed in the machinery to place the second or subsequent strikes, the floor worker has/had no idea what punch struck the die last. In the transitional years (1881, 82, 84, 86)where there could have been obv 1, 1a, or Obv 2 punches in use, you could get hybrids or scarce Obv/Rev marriages (1a/1, 2/1, 2/1a or 1884 Obv 1's or 1886 Obv 1a's. These also should be treated as major varieties because coins were struck with dies OK'd by the mintmaster but were different than the rest.
In answer to your last question, hybrids (1a/1, 1/1a, 2/1) were usually caused by different relief punches(call them what you wish) in the making of the working dies .. as I said before, it took multiple strikes to manufacture the working dies and they were not struck bam, bam, bam, but required periods of hardening and annealing as interim steps. Could some working dies have been struck with punches that already had errors/anonomlies on them? ... sure and you see it all the time where large numbers of coins all have the same repunched or re-engraved letters or digits. You can only take well-educated guesses on what went on on the floor of the Mint and Rob Turner's books will give you a pretty clear idea of what went on.
As you probably already know, Charlton's little guide at the beginning of each denomination to differentiate Obverses is not the best guide. It just follows a format that is followed through most of the book (hair & eye detail, lips/chin), not necessarily the best illustriative differences. You tell an Obv 3 from the long vertical cross-hatch on the E's and the almost-closed C's on the Obverse .. it has nothing to do with any facial features, except for the "mumps" portrait on some years. And you tell an Obv 2 from a 4 in the later years (where the dimple almost disappears from the throat) by the sweep up of the neck truncation with relation/closeness to the beads. Charlton is a guide, not the bible for ID'ing varieties. BTW, I was a member of the very small group that put together the variety section at the back of the 2011 Charlton .. I'm not a newbie or rookie.