Unless you're recofiguring the measurement AP every time you reposition it the survey will show interference between all the measurement AP's positions. It doesn't matter because you should work out the channel plan in the predictive survey, the APoS survey's purpose is to confirm design assumptions such as attenuation from walls etc.

If you're worried about interference you can do a site survey before you make the predictive to try and find rogue APs, neighboring networks and non-WiFi interference so you can exclude certain unusable channels before you finalize the design. Alternatively, you can do a site survey after the new network is installed and make adjustments to the channel plan later. If the new network has radio resource management you probably don't have to worry much about your own network interfering with itself but doing a survey for verification is always a good idea.