Is there any difference filing data for an in-transit shipment arranged by shipping line, vs, an in-transit shipment arranged by a freight forwarder where the master bill of lading terminates in the USA and all house bills terminate in the USA?

Is there any difference filing data for an in-transit shipment arranged by shipping line, vs, an in-transit shipment arranged by a freight forwarder where the master bill of lading terminates in the USA and all house bills terminate in the USA?

There is no difference. The key is that the house bill terminates in the United States, not in Canada.  In-Transit cargo is exempt from eHBL filing requirements.  [ref: Customs Notice CN16-23]