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This behaviour has not changed in VX.1, Packager has always worked in the way you are observing and has been discussed many times on Communities and in other forums. These are the basic requirements to ensure pin assignments stay as you intended if packaging connectors using single pin components.
Symbol placed with pin number assigned - Provide a Reference Designator to all of the symbols AND a Frozen Package = Fix property to at least one of them. Packager will not re-package the symbol with different pin numbers.
Or, new in 7.9.4:
Place symbol with pin number - Assign Pkg Group property with the same unique value, the value may be any text or number string you like. This will assign the same Reference Designator to all symbols with the same value leaving the pin numbers in place.