Unconventional Subwoofer Configuration
The SR6004's Speaker C setting is designed to let you bi-amp the front speakers using the main and surround-back outputs. For each channel, both outputs send the same full-range audio signal, and the bi-amped speaker must have an internal crossover to direct the highs and lows to the appropriate drivers. In your case, the subwoofer's internal crossover allows only the low frequencies to reach its driver.
To answer your question, the receiver does lose a bit of power when all seven channels are driven. Our measurements reveal that the SR6004 reaches 0.1% distortion at 73.1 watts with five channels driving 8-ohm loads and 1% distortion at 86.4W; with seven channels driving 8 ohms, it reaches 0.1% distortion at 70.8W and 1% distortion at 81.9W. More importantly, in your configuration, the sub is not receiving the LFE channel (the ".1" in 5.1), so you're not hearing the low-frequency effects in movie soundtracks.
You say you prefer the sound of the sub's crossover, but your configuration is far from optimal in other ways, so I recommend that you reconsider your strategy. I would definitely set the front left and right speakers to Small in the AVR and connect its subwoofer output to the sub's LFE input. This bypasses the sub's crossover, so use the receiver's crossover to redirect frequencies below 80Hz (or 60Hz if you prefer) to the sub.
If you have an A/V question, please send it to email@example.com.