Yes, but I don't think the MIDI settings are sophisticated enough to let you do it without a little bit of work.
The biggest hurdle is Local Control, which determines whether the keyboard generates sounds when you play it (Local Control On) or is silent when you play it (Local Control Off). According to the MIDI specifications available from the MMA (MIDI Manufacturers Association), the Local Control function is supposedly designed to toggle on and off either for individual MIDI channels or for all MIDI channels, but I've yet to see anything except "all on or all off" implemented on the Yamaha keyboards I have any experience with. So if you want to use the keyboard as a controller, you'll need to turn Local Control off, which means the auto accompaniment won't generate any sounds when you play it.
To get around that, you'll need to set up the MIDI software on your computer or tablet to receive and play the channels you want to use for controlling your software instruments (usually channels 1, 2, and 3), and send the channels used by the auto accompaniment (9 through 16) back to the keyboard so it can play them. That way the auto accompaniment can still be sounded by the keyboard as desired, although it will be in response to the MIDI coming back from your computer or tablet rather than directly in response to the keys you're pressing in the auto accompaniment zone.