You've grossly misunderstood... 3.3.5b does not go against being "blizzlike" as it is not the patch itself. What, however, goes against being "blizzlike" is suggesting that they enforce 3.3.5b changes on a 3.3.5a patch as it would not be accurate to the proper patch. Adding to that it is inefficient to enforce this on a 3.3.5a patch since you are better off changing the client altogether, you'd still need to patch the client as you are aware. Finally, they are planning to do cross realm features, once development allows for it, so they need to keep patches streamlined for these interactions.
That said they can't simply just change patches so easily since this isn't simply a matter of PVP anymore, there are just as many changes to be done in PVE mind you. Since 3.3.5a clearly has had more development to both servers it is understandable that it would become the mainstream, I mean AT only released 3.3.5b around August 2014 but how long has that been in comparison to their 3.3.5a development? There is obviously more sunk cost put in 3.3.5a for both parties.
Therein lies the other misconception... AT isn't the only one providing the fixes otherwise it wouldn't be a merger. Resources are shared and that includes the additional staff gained etc. AT may have its contributions no doubt but that doesn't mean they handle the matter in complete isolation from the existing staff on Molten. This is where streamlining becomes important, precisely to avoid a demarcation between AT and Molten staff as they are now co-workers under one server (Warmane).Since AT is the the one providing the fixes, it's my opinion that all realms should be moved to 3.3.5b but changed as necessary as to not ruin the "blizzlike" realms.
This should be the most important thing to remember this is not AT or Molten any longer but Warmane, so decisions are made under the banner of one identity and community.