I understand the interaction between the different rule sets. However, to me you are describing a Mage Wars rules supplement and not an Arena supplement. Adding sections of rules, codex, and clarifications to the Arena rules supplement to include Academy cards and Academy rule changes would be better communicated in a separate supplement just for that purpose. This makes it easier for customers to understand the different options in the product lines.
I think we may me talking across purposes. What I was talking about (and understood others to be) was talking about Academy cards, and rules and rulings on those cards in Arena. As such it has nothing to do with Academy at all (other than Academy being an expansion for Arena) and would still be a purely Arena document...
In principle, for both Mage Wars product lines to exist and prosper, there needs to be a Codex/Rule Supplement/FAQ for Academy (eg the game itself, and rulings for cards and card interactions in that format), and a separate Codex/Rule Supplement/FAQ for Arena, which includes rulings and effects for all cards legal in Arena (eg including Academy cards). Stagger has already made an appearance in Codex v 3.1, and it has been stated that Azurean Genie's wish action is a quick action, etc, and I could envision other Arena rules questions about Academy cards that only apply to Arena (eg can Jade Gremlin's mana-paid effect dodge Wall Passage attacks? Bash attacks from being pushed into a non-Passage wall? Attacks from Damage Barriers? Zone attacks and other Unavoidable attacks?).
Sadly, it is clear that Arcane Wonders is unable to support their flagship product line by keeping up with FAQ and Rules Supplement documents, card database, spell book builder, organized play event kits, web site updates, etc. Either it will fall on fans to make ruling compilations and their own spell book builders and card databases with scanned card images and unboxing videos, or the game will continue to along the path towards a slow death due to lack of official support.