I work on a large scale, high volume, public facing web application. The successful operation of the application is very important to the business, and so there are a number
Either option would technically work, although the solution could come down to how your organisation feels about page validation.
As you say, adding information into custom metadata tags will invalidate your markup.
For my organisation, page validation is part of technical accessibility and is considered very important. Doing anything that would prevent pages from validating would not be allowed.
I wouldn't attempt to register new metadata names and values as these are specific to your organisation and not for public use.
I would probably leave this information as HTML comments if this is already working for your organisation.