Hi. Do you have your front speakers on the Pioneer set to small?
In options 1, 3, and 4, the signal sent to the integrated amp is full range, so your front speakers will be playing all frequencies. Unless I'm remembering wrong, Pure Direct on Pioneer receivers still applies bass management. So, if you have your front speakers set to "small" on your Pioneer, option 2 would not send anything below the crossover frequency (e.g. 80 Hz) to the front speakers, likely causing them to lack "depth" as compared to the other options.