There may be to much in the joist spaces that would not allow for rectangular duct runs. Things like electrical boxes, water lines, drain lines etc. Some times these things look easy until you actually have to do it. It sounds like your HVAC people are on top of the duct sizing issue and want to be sure airflow is not short changed. You may want to get another opinion. Be careful though there may by someone out there that says they can do it without the proper research. Along with the duct being installed in the joist space insulation will probably be needed also which will reduce the rectangular size creating a need for more runs than you think.
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