Turborascal, pretty sure you are right, although there could also be button compatibility concerns (for example, can the trunk button on this new Mazda3 remote be made to work with the cargo door on the CX-5?)--but I'd assume that has less to do with physical keys and more just likely with the protocols involved.
Personally, while I am not a huge fan of the Mazda capsule style smart keyless fobs (had that same general style I think on my 2010 Mazda6 and my previous and current CX-5), this new MZD3 one looks ginormous, and from what I saw on a related YouTube video, the physical key is inside and you have to open the case to get to it. It is certainly a more visually attractive design however, and one might argue the side button designs might result in fewer accidental presses. I think my favorite Mazda smart keyless fob was my 2006 MX-5's, which was the lightweight credit card style one with the flat key that slid out. Easily fit in my pocket with no bulges, and even the key itself had a completely flat head.