Are you saying the edges of the tiles at the opening are beveled, or are you saying that in plan there's tile in the way, i.e. the opening is a rectangle with a corner cut off? A picture would help clarify.
So you're thinking of setting the new base on the top of the tile? Are your sure the cast iron glazing goes all the way to the very bottom of the unit, and that there isn't an unglazed 1/8" or whatever at the bottom? Because the usual thing is to set the tub/receptor on the subfloor before the finish floor is installed, and the the finish floor butts up to it.
If your wall has a 2" jog in it, there are certainly ways to handle that gracefully, if you'd prefer to have a knee wall with glass on top.
Also, you might consider the option of setting the receptor back against the existing framing, and dealing with the gap in the tile somehow. E.g. find a closely matching new tile. Or (very hard) non-destructively remove the tile under the new flanking wall between the receptor and the toilet, and reuse it. Or cut the tile back and infill with a coordinating tile material.
Cheers, Wayne