This deserves a full reply! :D
Considering the absence of a board diagram, the "Fire and Shrapnel" example mission does not have one. The assignment rules state to use provided template without changing the format and to stick to standard OPR mission format. So it is a conscious choice to write about all the markers placement in text.
About the book keeping, a color coded die next to or on a marker easily solves that problem. It is the only "moving part" of the mechanic.
About the shelter entrance marker, I agree, the following wording would be more suiting: "...that unit is removed from the battlefield scoring 1VP."
Last but not least, the Secure and Protect - I decided on this form of notation, as I noticed, that Gaetano assumes a level of... logical approach to the topic from his players, across all themes and systems in OPR. Your critic is valid from a designer standpoint for making the rules foolproof, at the same time the cumulative effect isn't clearly denied, therefore it applies as a logical conclusion, which goes with the overall OPR rules flow.
Thank you for taking the time to leave a comment, much appreciated!