What are the leading bytes before the USB setup
These bytes are the descriptor data returned by your device in response to GET_DESCRIPTOR request. These data can't appear before the start of control transfer, something is missing in your observation.

The host must start with SETUP transaction [2D]. Then the setup data should follow:

[C3] is DATA0 token, [80 06 00 01 00 00 40 00] is "get descriptor", [DD 94] is CRC16.

This SETUP token must have ACK from your device.

The host then should proceed with IN token.

The device, in response to IN token [69], should always return the result, which is [12 01 00 02 ........]

"12" means that the descriptor contains 18 bytes of data. The rest you would need to decode, preferably using a better tool, like Teledyne-LeCroy/CATC decoder.

In particular, bytes[8..9] [E6 04] mean the Vendor ID = 0x04E6 (
SCM Microsystems), the next 2 bytes [16..51] means PID=0x5116 - product iD (SCR3310 SmartCard Reader), the rest are other standard fields of your device descriptor.

[D2] is ACK, which is good.

Here is an example of GET_DESCRIPTOR transfer from a LS mouse:



The descriptor data (18 bytes) are split by host into 3 transactions, because of max_packet_size is 8 bytes only for this particular device (Logitech mouse). The whole transfer also has several NAKed transactions, which are hidden.