Include all choices. Follow the rules in the general style guides and modify them if they are in conflict with your company's style guide or industry standard. There are no choices, and only one set of rules applies. Everything must conform to consistent grammar and punctuation rules, even if changing the wording in the text may change the meaning a little. Consistency is important, but do not change the meaning.
Consistency is never a problem if good sentence structure is used.
The comprehensive it is bigger. The house manual it is more specific to your document. Neither always make up your own rules. Consult both the comprehensive and house manuals and decide based on how appropriate each manual's answer is to the specific question. List every detail of every edit you make.