To my knowledge that's not possible. As you say the HWP is directly linked to its weapon (units: and items:, items: includes tu costs, etc.).
What you can do is to fill both the unit's hands with items using builtInWeaponSets before the HWP weapon is being added. Another solution seems to be have an AI soldier type and have armors for that soldiers type.
For example X-COM Files does that. I believe it's the Enforcer armor that has free hands.