Depends... you have to deside what extra updates to not use from the normal rules and what leave.
So that you don`t get douple power, card or skill upgrades, but get boon upgrades. Some tinkerin is needed, but it is possible. But personally I would play the box game normally and leave sosiety rules to sosiety adventure paths because those have been balanced to character decks. IMHO. But I am guite sure that sosiety rules would work just fine in most cases with reward tinkering. Aka only one power, one skill, one deck size upgrade per level and none of those in 0 level scenarios. Leaving only boon upgrades from the box rules.
I think that there are two shortcomings in this plan:
- thinking that the cards in the CD are the only cards that meet the "theme" of the character, and
- ignoring the theme of the adventure, which is often augmented by the boons available as part of the AP
The only aspects of Society rules that I would apply in standard AP play would be to modify the boons upgrade rules, but only for those instances where the reward is a random boon from the box; and to allow Loot to be used in a manner similar to Society play. In the "random boon" instances, I would allow the player to pick an appropriate boon from the CD. I would leave all other rewards as normal, and I would retain the standard rules for rebuilding a deck with the boons acquired during the scenario. I would not "rearrange" the rewards to the Society model - simply use the normal scenario rewards and allow the loot/random boon changes when those are the scenario rewards. In theory, this would preserve the character advancement potency with the scale of the challenge for the AP.
My solution is kind of a hybrid from the normal practice in which you would simply shuffle your CD cards into the AP box, hoping to acquire the boons during the course of the adventure.
I see the CDs as presenting a "standard" progression for a character in a generic environment. However, as with real life, one's experiences can shape one's progression. So CD Valeros going through the Skull & Shackles AP is naturally going to progress in a manner different from CD Valeros going through the Rise of the Runelords AP. They are facing different threats, meeting different individuals, and have access to different equipment simply due to the nature of where they are and what they are doing. Some of those non-loot boons are actually useful in the AP. Limiting characters to the CD boons seems overly restrictive. So using the boons from the AP allows you to explore small variations in character theme. Those variations aren't in any way violations of a theme.
The very nature of Society play doesn't allow for normal scenario rewards to be used (the normal AP concept is that all of the characters are tackling each of the scenarios in sequence - Society rules have to allow for a much more ad hoc play concept). The strength of being able to choose a boon from the CD offsets not being able to keep the AP boons. The CD boons generally aren't optimized to the AP's theme, but they are generally useful. Part of the fun (to me) is encountering one of those nifty AP boons and scrambling to acquire it because you don't know when someone is going to encounter it again. That sense of urgency is lessened somewhat in Society play because you don't need that card - you're only trying to get a boon of the same type and level.
As always, however, it's your game and you can play it any way you want. You may find that your idea is fun to play (for you and the rest of the group). If that's the case, go for it.
The short answer is that, in my opinion, you're not making your characters overpowered by doing this. As long as you take the official PFSACG rules and only take one permanent card upgrade per scenario, based on the cards you acquired.
By taking these rules, you tend to have a much greater chance that you'll find something to directly improve your character rather than the mishmash of boons you get in normal play. I personally feel like this somewhat limits the experience and your own personal creativity, but I can also understand the appeal of a more structured, defined 'progression' offered by the PFSACG rules.
With that said, 'overpowered' is a relative term. The card upgrade rules are unlikely to seriously affect the game balance (except MAYBE in conjunction with Mummy's Mask Traders, depending on how you implement them), but which Class Decks you pick almost certainly will. If you play a Fighter, Rogue, Wizard, Sorcerer or even Druid Class Deck in Wrath of the Righteous or Mummy's Mask, you may find that your own Class Deck boons are quite measurably weaker than the cards in the actual box, and you may be playing with a weaker deck as a result. On the flipside, if you use Pathfinder Tales or Hell's Vengeance or an Ultimate Add-On deck in Rise of the Runelords, you're going to be playing with far stronger boons than the box will generally provide for you, with some exceptions.