I was downvoted (unjustly) when I mentioned App Sandboxing the other day (here: http://news.ycombinator.com/item?id=4004833). Apple will force sandbox effective June 1st, so they can't provide updates through MAS version if Coda 2 is not fully sandboxed. They haven't said anywhere whether that's the case or not.

The support page says:

    Apple often changes the conditions for Mac App Store eligibility, and it's possible
    we may have to modify or remove features from the Mac App Store version in the future. 
    It's our intent to keep them as close to identical as Apple will let us.

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So, they might be forced to remove some features from the MAS version, in that case, it'd be better to get it directly from panic.com. On the other hand, MAS version sports iCloud support, so if it's fully sandboxed, it's better to get it from MAS.

We can wait a few weeks to see which on is the case, but in that case, we'll lose the $50 discount.

I'm sure Panic is aware of all these issues and doubts, but I can't think of an honest reason why they don't address these issues.

I love Panic and their softwares; that's why I hate to see that they're apparently playing with their customers.