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Not an issue with PKHeX; this is how HOME behaves when you skip the legitimate means of transfer (Gen7->Gen8 via HOME). HOME does not have the initial data to compare to, so it leaves it in a default ball when transferring.

that is a good sharing which is really helpful as well

No, since gens 3-7 can produce shiny Pokémon that don't have an XOR that 0 and square shiny Pokémon need the XOR to equal 0. Gens 3-5 can have a XOR of 0-8 and Gens 6-8 can have a XOR of 0-16 for a shiny Pokémon to be produced. The exception to this is virtual console Pokémon, Fateful Encounter Pokémon, and Pokémon from GO will always be square shiny. Another exception are Max Adventure Pokémon will have a XOR of 1 so they can never be square shiny.