A lot of thoughts going on in your post but I'll try to answer the question I think your asking.
When you create a baseline system using Appendix G you only use one of the eight baseline system types specified. There is not a DOAS - CV FCU baseline system so you never have to worry about this as the baseline condition. Your baseline system will be either a CV single zone or a VAV multi-zone and in either case it is assumed that return air goes back to the AHU rather than staying at the zone level. You will want to re-evaluate the conditions requiring heat recovery after you complete the sizing runs of your baseline HVAC systems making sure that ventilation rates in the baseline are the same as in the proposed design.