This is not true. All uploads are run through YouTube's Content ID system whether you are with a network or not. However, there are a few channels who fall under the "Managed" status that may not get screened. That being said, those Managed channels still have to be careful about uploading copyrighted content.
The original reason for YouTube to allow networks to instantly monetize was that the networks were supposed to screen their partners. Needless to say, the networks weren't screening their partners so the networks lost the perk of allowing their members to instantly monetize the videos.