When a player is using the "autowalk" feature, Minetest does not set the "up" bit in the result of minetest.get_player_control_bits().
I believe this is not intentional, as the "autojump" does set the jump bit when it triggers.
It is unclear to me if those features should, to all intents and purposes, behave like they were "pressing keys" for the player. I have observed that players may open their inventories or even chests and furnaces while the autowalk function is on, something they cannot do with keys (i.e. pressing movement keys while a formspec is shown has no effect).