In the Introduction to the MPEP (or whatever prefatory section is preferred), add a short section on which terms are requirements and which describe best practice.
Those without legal training sometimes interpret the term "should" similarly to the term "must." This seems to lead to confusion and complaints from those MPEP readers that the MPEP is "confusing" or "self-contradictory."
Although some readers of the MPEP may not have legal training, most have some science or engineering training. It may be helpful for those readers to put in a short note about the effect of certain terms, similar to those used in engineering standards documents. One example can be found at https://www.ietf.org/rfc/rfc2119.txt.