Your architect has to 100% know the thickness of each of your floors for each area, which means you have to 100% decide on that before getting plans done. Then he can specify different joist heights for the different areas as needed and the details needed to be able to do that and not have everything else be off.

If you can't do that, then you're probably going to end up with at least a couple of thresholds. It's not a flooring guy's responsibility. It's the architect's.

Any flooring professional ought to be able to give you flush surfaces where each product meets another. It might require the installation of underlayments to do that. Expect increased costs for the underlayments.

It is not rocket science. Read the architect plans to see what is listed as to be provided for the finish flooring; that will tell you what is planned. Then, you (or the flooring installation contractor) need to know the various flooring thicknesses and what underlayment and trim pieces will be required to give you a flush walking surface, as well as a visually acceptable result.

Some 'trim' pieces may be unavoidable. Howewer, in new construction "saddles"...unless they are wanted...are ridiculous, except for those included at exterior doors. Trim pieces can be of many different profiles and made of different materials (metal, wood, plastic, marble) and of different widths. Don't accept metal 'binder bars' that are fastened with screw type nails to function as joins between two dissimilar materials...talk about UGLY!