Can I get by with two thin layers of thinset for both layers in order to have a perfect match on transition?
The thinset under the hardi will compress to about 1/16" thick, but under the tile, you will need enough thinset to achieve 85-90% coverage on the back of the tile (You strive for 100% coverage) but expect you will have 1/8 to 3/32" in thickness of thinset under the tile once set. You can't skimp thinset coverage in either place and a 1/8" difference in floor elevations won't even be noticed.