Very likely, familiarity with the Motorola environment and Motorola as a supplier within the development staff might have been technical reasons for choosing that CPU. After all, quite some of the designers had an Apple background, just like Jobs himself. But I don't think basing NeXT on Intel would have presented a major technical problem for any of their developers above maybe minor inconveniences (Keep in mind NeXTSTEP for Intel became available 1993).
Beyond technical reasoning, I would assume marketing reasons were considered much more important.
Looking at the first NeXT presentations, you can easily see that the Next ecosystem had the intent to appear as something revolutionary, new and ground-breaking, throwing all of the "old and awkward stuff" out of the window. The NeXTSTEP environment was demonstrated (quite credibly, at the time) as a revolutionary object-oriented and entirely user-friendly (and, admittedly, "exotic" and "luxury" - to justify the price point) combination of hardware and software.
Considering these ambitions, the added capability to be able to execute "boring old DOS programs" like WordPerfect or Multiplan would rather have de-valued the platform than been seen as added value, and, more importantly, would probably have encouraged reviewers to directly compare NeXTStations to high-end PCs, both price- and performance-wise, this totally defeating the ground-breaking targets (and, obviously, also eroding their $$-value). After all, DOS programs would in no way have profited from NeXTSTEP. Next wanted to be clearly distinct from the PC market, not integrate with it. So, the ecosystem targeted not at competing with high-end PCs, but rather at markets above.
I think it must be noted that this actually seemed possible at the time NeXT was active. The high-end DOS/PC platform was by far not as prevalent and "standard" as it was in later years, thus that marketing policy was probably even reasonable (and resonated quite well in the higher-education and academic research market, for example, and, as such, worked at least for some years).