OK, taking these one-by-one
What crossover freq for all my speakers?
I would recommend 80Hz across the board there, but you should simply experiment with 60 vs 80 and see which sounds better to you. There are several important advantages to redirecting more bass to the subwoofer channel, most importantly (1) shifting a larger portion of the troublesome low freq's to the higher resolution MultEQ filters in the SW channel and (2) freeing up headroom in the AVR's amp section, as the most energy-greedy low freq's are handled by the dedicated amp in the subwoofer.
To me, it seems like the fronts should be at 60 and the backs at 80. Is there any physical harm or problem to look for by setting them all to 60 though?
no, not at all, as Audyssey has measured that your speakers can play down to 60Hz in your room.
This leads into my next question about double bass with LFE+Main. Your guide seems to stick towards using LFE only if you have a subwoofer, is this just because of the quality of the bass. Does bass become distorted when combining from two sources that aren't identical?
Double bass is a useless setting, it only exists because of consumers who felt insecure about setting their big tower speakers to "small" and so they were given an option that would allow them to set their speakers as "large" and yet still have some bass redirection to the subwoofer.
The problem is that your main speakers simply cannot reproduce the low bass frequencies as effectively as a subwoofer. And, when you engage double bass, you will no longer be getting "flat" bass as the multiple bass sources will overlap... but then the speakers will run out of steam around 60Hz, so you will have some "overlap zone" but others which do not overlap and you will get an unnatural hump in that overlap region.
Multiple bass sources are actually a good thing, having two or three subwoofers is a proven way to diminish room acoustic problems. But they should be EQ'd together as one dedicated SW channel, that is not the same thing as pushing your tower speakers with a "double bass" setting to ranges they can't actually reproduce.
Audyssey determined my speaker distance very accurately accept for the subwoofer.
sub distance is covered in the FAQ
this is very common and is because of the delay caused by the internal circuitry in the subwoofer. the measurement is not actually distance, it is just a proxy for "delay". the point is to make sure the TIMING of the various speakers is accurate.
Oddly, it determined that the subwoofer about 3 feet further than it actually is but it also decreased the db by 7.5. I would have assumed an increase in db if it's registering it further than it actually is.
one has absolutely nothing to do with the other -- the channel volume will be set at the point required to make that speaker play at the same volume as the others (as measured at the 1st microphone position).
How do you know an acceptable volume limit?
as long as you aren't going far past zero you are pretty much safe. The receiver will let you know if you go too far by shutting itself down into protect mode. But, in general, as long as your ears aren't bleeding you are probably not at any risk
Remember that the toughest freq's are handled by the sub's amp if all speakers are set to small.
different sources will have different volumes, so the range you describe is pretty normal. Movie sources are the only standardized volumes, a volume of -30 to -10 is pretty normal for home veiwing, but nothing wrong with pushing it closer to 0 if you really want to feel the action!