@ zionfrost your most welcome.
Quck brief answers;
1) yes they both have an os & no different os , linux modified aka android os so a difference
2) if stock all market apps u can back up (google also keeps back ups, look in settings). u can connect your microusb to your pc & copy & move some apps & data. but, if rooted, best way you back back up all apps & data if you buy titanium backup, mybackup pro etc on market.
3) suggest more reading manual, here, xda & other forums & u-tube
Once you do a little reading you will see all these simple answers & have a better understanding
since your technically minded already its just reading & some youtube vids for u
hope that helps