IIRC, the switches are there to avoid broken markup when tagx files are used in jsps that have no markup. This occurs particularly, when entities are used as subentites of some other entities (e.g. authors are Persons, that might or might not be part of a publication). Aligning the tagx structure with the entity-field-structure of the markup is non-trivial. I would suggest to keep the switches (actually to re-introduce them) in tagx files that are used on pages with and without markup. They should be kept until the there are no longer pages without.
The only switch allows us to disable the markup for the template that is used when the comment is posted using AJAX.
Search engines never see this dialog so in my point of view this switch is useless.