How to level bathroom plywood subfloor before tiling?
You could do either:  


level the floor or 
level the individual parts (shower enclosure, vanity, toilet)


Which you choose will depend on the degree of out-of-level

Self Leveler:
self leveler does not need to stay intact after the backer board install.  It can fracture and still completely support the backer board.. its got nowhere to go and it doesn't migrate or degrade.

My personal preference is to use self leveler and then use a crack isolation membrane.
(Ditra is my preference, comes in 1/8, 1/4 and heating wire support styles)