Curious... I've never used i3 but the functionality is pretty much plain Gtk+ (when the autohide timeout expires, the panel window is moved offscreen to x/y -9999/-9999 and the 3px tall autohide window is moved in its place).
I have the same issue. This appears to be the relevant debug log output from i3
09/19/2020 09:12:19 AM - handlers.c:handle_configure_request:279 - window 0x02807428 wants to be at 0x1077 with 1920x309/19/2020 09:12:19 AM - handlers.c:handle_configure_request:312 - Configure request!09/19/2020 09:12:19 AM - handlers.c:handle_configure_request:362 - Reconfiguring dock window (con = 0x55c20bedfdc0).09/19/2020 09:12:19 AM - randr.c:get_output_containing:118 - comparing x=0 y=1077 with x=0 and y=0 width 1920 height 108009/19/2020 09:12:19 AM - handlers.c:handle_configure_request:386 - Dock client will not be moved, we only support moving it to another output.09/19/2020 09:12:19 AM - xcb.c:fake_absolute_configure_notify:85 - fake rect = (0, 0, 1920, 3)09/19/2020 09:12:19 AM - handlers.c:handle_event:1358 - event type 23, xkb_base 8509/19/2020 09:12:19 AM - handlers.c:handle_configure_request:279 - window 0x02800007 wants to be at -9999x-9999 with 1920x2509/19/2020 09:12:19 AM - handlers.c:handle_configure_request:312 - Configure request!09/19/2020 09:12:19 AM - handlers.c:handle_configure_request:362 - Reconfiguring dock window (con = 0x55c20bf23f30).09/19/2020 09:12:19 AM - randr.c:get_output_containing:118 - comparing x=-9999 y=-9999 with x=0 and y=0 width 1920 height 108009/19/2020 09:12:19 AM - handlers.c:handle_configure_request:386 - Dock client will not be moved, we only support moving it to another output.09/19/2020 09:12:19 AM - xcb.c:fake_absolute_configure_notify:85 - fake rect = (0, 1055, 1920, 25)09/19/2020 09:12:19 AM - handlers.c:handle_event:1358 - event type 22, xkb_base 8509/19/2020 09:12:19 AM - handlers.c:handle_configure_notify:1131 - ConfigureNotify for non-root window 0x02807428, ignoring09/19/2020 09:12:19 AM - handlers.c:handle_event:1358 - event type 22, xkb_base 8509/19/2020 09:12:19 AM - handlers.c:handle_configure_notify:1131 - ConfigureNotify for non-root window 0x02800007, ignoring