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 count

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.