the tang of the cheese flavor, the softening time on the dough would be the major differences and the filling on #2 has less fat (but it's rugelach, who's counting???)
What brand of margarine are you using could it be SMART BALANCE?
You could change out the butter for margarine for sure but the butter may have less moisture, in this type of cookie, I don't think that would read as a bad thing. May give you better color too.
My question to you is why the change? Do you have cream cheese and butter in the house and need to utilize or are you having a taste test?
How is that book in general?
I love getting ready for the holidays, all of 'em.