picture would really help, but you could just cut the trim going over the tile 1/4" short and your trim would be level for the entire building's floor. it might look funny going up and down 3.5 deg all over the place. just scribe that transition slope for those pieces.
i scribe almost everything. put in the pieces that are on the wood floor and tiled floor. take your transition trim and flip it upside down and moulding faced in, scribe a line from the top of the wood side trim to the tile side trim. rip it on a table saw or whatever.
trim before flooring kinda seems like putting on a toilet first and then sticking your tile underneath it, but i'm a maintenance person and have never built new.
the one time i installed a new bath floor, i definitely did the ply, thinset and tile, cabinets, baseboard, then toilet. usually the flooring is already there.