Does an Autonomous AP have the ability to send a packet from a source in the BSS directly to a destination in the same BSS, without having to strip off the 802.11, replace with 802.3 and send to a switch? Would this have to DS=0, from DS = 0?
Yes, this is called "Intra-BSS Relay", and it is standard operation for all APs.
When clients A and B are in the same BSS (i.e. associated to the same AP), when client A needs to send a unicast packet to client B, it actually sends it to the AP. On this leg of its journey, it's ToDS=1, FromDS=0. Address 1 is the AP's MAC address (BSSID), Address 2 is client A's MAC address (Source) and Address 3 is client B's MAC address (Destination). If WPA or WPA2 is in use, the packet is encrypted with client A's unicast key and cipher.
Then the AP relays the packet to client B. On this leg of its journey, it's ToDS=0, FromDS=1. A1 is Client B's MAC (Destination), A2 is the AP's MAC (BSSID), and A3 is Client A's MAC (Source). If WPA or WPA2 is in use, the packet is encrypted with client B's unicast key and cipher.
The AP is always considered part of the Distribution System, even if it is completely standalone and not connected to any kind of backhaul network.
The 802.11 spec is independent of 802.3 and does not require any conversion of 802.11 headers to 802.3 at any time. Technically your DS, if any, needn't be 802.3 at all. However, most real-world devices that contain an 802.11 AP use 802.3 as their DS network, so those devices must translate packets to 802.3 if/when they need to be forwarded onto the 802.3 network.
You asked about ToDS=0, FromDS=0. That's used in IBSS (an ad-hoc network with no AP, thus no DS). In an IBSS, all peers send direct to all other peers because there is no AP to do IntraBSS Relay.