They are responding to the very recent emergence of applications (like Firefox) that (optionally) use their own encrypted DNS, thus bypassing the enterprise's ability to apply security policy based on DNS. (Visibility on DNS is also useful to help detect some malware.) I'll allow it.
They aren't recommending you don't use DoH. Just that you don't allow individual apps to bypass your enterprise resolver. In fact I use the same strategy at home (with DoT) to enforce ad and tracker blocking. It's just common sense really.
From the document:
>[...] NSA recommends that the enterprise DNS resolver supports encrypted DNS, such as DoH, and that only that
resolver be used in order to have the best DNS protections and visibility.
