Id Software's history at that point (commander keen, wolfenstein, catacomb, doom) was entirely on x86 MS-DOS and they were exploiting all the tricks to achieve decent performance for games thought to not be possible on that platform.
So it seems very unlikely (to me) that they would develop the games first for a different platform, using a different OS, on a different CPU, with a different endianness.
They developed Doom on NeXT with highly portable C code. The reason for that is they were more productive on NeXT workstations (development and map design). Doom has been easily ported to every platform because they designed it to be easily ported. Recommended reading: https://fabiensanglard.net/gebbdoom/
Not only that but it was due to their portable software architecture which was by design. Carmack isolated the platform dependent stuff so that you can port it to any other platform without too much effort.
The great majority of platform dependent code is video output, keyboard handling, sound and network.
The functions for that that call dos/x86-specific code are neatly separated by the rest in appropriately named files, so it’s really easy to know what you will need to modify, without a million other distractors.
The difference is that the id devs had already come from the Apple II world first, so they had written plenty of 6502 assembly and were aware of the cycle counting types of optimizations, but chose to give some of them up to use C when they started on x86. That was, at the time, a relatively bold move.
By the time Doom was being made they definitely had a sense of what a high-level approach brought to the table, and that they could focus on just the "hot loops" for micro-optimization when targeting a 386. The process they were using to build their engine was ultimately iterative in nature, building some tools and some rendering and some assets, then gradually pushing each a little further: the introduction of the BSP algorithm came relatively late, for example.
So it seems very unlikely (to me) that they would develop the games first for a different platform, using a different OS, on a different CPU, with a different endianness.