This has always been a bugbear everytime I compile a schematic and get tons of these types of warnings. What on earth are they talking about ?? Even the Altium online help does not make it clear what is going on with these warnings. This concept of viewing mode of the parts in the library was totally foreign to me until I came across across this website and explanation and now it makes perfect sense !
http://www.programmersought.com/article/89083545460/I managed to clean up the library by deleting alternate modes with bogus footprints and pins thus reducing the number of warnings ! Now most of the warnings remaining are things like power ports connected to passive components flagging a floating port error etc.
cheers