I'm sure there are more non-standard variables but here are the ones in my particular build I have notice do not jive well with the standard base maps.
High Compression (anything 11:1 or higher)
Cold running motor (my motor for instance takes 20 of the 25 min of my ride into work to get the oil temp above 180 degrees)
Extra High gearing through final drive ratio ( I run a chain 24 tooth tranny with a 48 tooth rear sprocket, which gets great fuel mileage (165 town/210 highway) However on a +130/130 build the amount of actual twist of the throttle it takes to keep it moving is so minimal it seems to make it run more in map areas it was not set up to cruise in for instance I turn 1800 rpm at 45mph in 5th and 2k rpm at 55.
Would like some opinions on how everyone thinks these things effect the autotune procedure.