The question is understandable because EMM/EMS use protected mode in a limited way.

In fact, 386 protected mode could still make use of memory segmentation, with 32-bit segment registers being an upgrade from the 286 protected mode.

But there has been no production OS that continued to use segmentation once 386 mode made 32-bit addressing so easy. In large part because Unix could be ported from flat memory models such as VAX, and m68k.

Therefore, since CP/M-386 is derived from CP/M-68K, it seems straightforward that a flat 32-bit memory model is employed.