Again, boxed Pokémon do not store the current stat values.
PKHeX works by loading the Pokémon's data from box, then checks if there's any existing stat values to display. If there are none, it regenerates them based off the game's stat calculations. Then, it shows the stats. If stats were available (eg, read from a Party slot) it would show those instead.
Since no stats are stored in the box, the program regenerates them instead of showing nothing/zeroes, hence things differ from what you see in-game.
All PKHaX does is just allow you to tick "manual stats", which disables the program from recalculating them when stats already exist (party) or when you change other stat-influencing things like Species/Form/Level/etc.