"Furthermore there are a lot of other things you have to put up with that you might find silly like religious sayings, or prayers before meals, or whatever else and you have to put on the fake smile and not comment about it because you don't want to be rude. It just seems like the whole thing, if it works, must be phony."
1. I come from one of the most historically-conservative, Bible-banging districts in California...I get to spend most of my day out of that area, thankfully, but I still live there. Suffice it to say that I've had a lot, A LOT of religious friends, deeply religious, "I believe in Creationism" or "I believe Joseph Smith was right" religious.
And never...*never*...NEVER have I seen someone actually pray or say grace before meals outside of the Passover Seder.
But even there, I sit there because, damn it, my grandma's 90 and you love your grandmother despite disagreeing with the religious side of Jewish history, so you sit there and genuinely love your grandmother while doing this for her. It doesn't mean you don't genuinely love her, it means you love her genuinely ENOUGH to where you're willing to go through the motions for her AND she's willing to acknowledge that, yes, I'm going through the motions and don't believe, but she's mature enough to handle that and love me anyway and appreciate the gesture.
Likewise, if I had a friend who actually DID do the whole "saying grace" thing before a meal, and insisted I do it--sure, why not? They know I'm not a believer--it's not as if I'm particularly shy about my being an atheist Jew, right?--so I'm not fooling them, but it's a sign of respect to go along with their tradition.
And it's a sign of their respect that they won't demand that I convert, or call me a heathen or say I'm going to hell just because I don't believe.
THIS. ISN'T. HARD. You're treating what amounts to a Comedy of Errors like...the kind of overly-melodramatic fluff which generally make up a comedy of manners.
2. How is it phony, when the basis of our friendship is something other than those religious tenants?
If I had told a girl I liked I was totally 100% Catholic just to date her and THEN went through the motions, then yeah, that'd be phony, because the basis of our relationship BEGAN with a lie, my saying I was Catholic which (spoiler alert) I'm not.
But my friendship with all those people are based on other common interests, so how is it phony to say "You know that belief you have? I disagree with it" and have them say "OK then" and you both continue on with that friendship built upon a foundation which is not religious, thereby making religious disputes ancillary to the main relationship?