I think a common misperception is that one can transfer miles between programs. True, there are legal and sneaky ways to do this, almost all resulting in loss of miles.
Just like some people use the terms "nonstop" and "direct" flights interchangably even though they don't mean the same thing, "transfer miles" may be similarly confused.
Many airlines' ff programs allow you to get credit for flying another airline IF you give them the correct ff number that you want credit. For example, you can give AA your AA number OR Alaska number (not both) and the miles will go to the program whose number you gave.