The main difference is standard vs proprietary communication protocol used.
Also term protocol integration could refer such to variety of products/servers/services.
For example you can make such against Management Server / Recording Server, Mobile server, ONVIF Bridge / RTSP server, DLNA server etc.
Could you elaborate a little bit more on what you are trying to achieve ?
In this way we could try to advice you for the possible / best / easiest integration.
You mentioned Web client and ONVIF bridge. I could assume your are in doubt between Mobile server and ONVIF/RTSP integration. But this is only a wild guess.