Last bits of config. bitstream are ignored in Passive Serial Configuration

Those are simply padding bits being transmitted by the host until it receives the CONFIG_DONE signal, or until detects an error condition.

If you take a look to data line, you see a sequence of 0xFF bytes.

This is usually done because some devices need extra clocks for startup timing.

The 'substantial' bitstream required for fpga configuration has actually finished a few bytes before you see CONFIG_DONE going high.