Can the compliance testing for the military standard MIL-STD-704, specifically section 5-2-3 and 5-2-4 related to avionics testing, be conducted using PCR-LE series and the optional SD012-PCR-LE/WE (avionics test software)?

Yes, it is possible. Additionally, PCR-LE series supports three-phase output testing.
Please read the operation guide of SD012-PCR-LE/WE (avionics test software) for the details.