If they laid the tile with paper, they probably didn't know how to get
a non-flexing floor to lay it on. If it's just plywood over joists
(16" OC) in a stick frame, the subfloor should be at least 1 1/8" thick
plus a 1/4" layer of cement board (Hardibacker is my favorite). If you
want to use mastic and stick with the small tiles (up to 2") then the
floor movement is of less concern. Also, as far as a new floor lining
up with other things, the doorway is your biggest concern. A big
difference there will have to be transitioned with a threshold. Takes
some skills to cut and fit that. Being level with the flange is not as
important. If you end up a bit high, use double wax rings to ensure a
seal. Around the trim, lay the tile to within 1/8" and fill that gap
with caulk that matches your grout. TEC brand is good for this, get it
at a tile dealer. It's more expensive than the crap box stores sell,
but for the amount you'll use in a bathroom it'll be worth it. Good
luck!