Yes, you are correct regarding average scores.
The text of polymorph any object states you also get the int of the new creature, not the higher of the 2...
Per the spell you gain str, dex, con & Int of the new form. (Roll for the new race) Nothing in the spell description allows you to opt out. Roll 4D6 drop lowest then apply racial mods.
It's DM call on allowing you to keep or gain racial abilities.
Not directly. It depends on the composition of the PCs. If you are using core characters with standard wealth/level & standard char generation then use CR & the encounter tables and it will be fine.
I don't get involved in intra party matters. I have no idea if the players use these skill rolls. I only get involved when NPCs & monsters interact with PCs.
DM's don't run PCs.