All of your suggestions are wrong!
First, do not put backer over greenboard. There needs to be a vapor barrier behind the backer, heavy mil plastic or 15 lb felt. 1/2" cement board is the better material. But in any event, the backer does need to overlap the tub flange. You need to fur out the studs with lath spacers so the the backer board sheets hang plumb. All seams and gaps in the backer installation are taped with fibrglass tape and waterproof joint compound, or thinset.
For excellent further advice on your project, check out this tile forum: