The PCM - bit stream merely allows for another decoder to handle the decoding/output. bit stream ususally is the preff'd setting for say a receiver to do multi ch.
PCM usually is the setting for many DACs, and or, analog output from that source. This goes for either CD or DVD
AS for all the other upsampling choices, I say try 'em all. As you have already noted, some settings will do one thing for you and other's will uh, be different.
I'm not terribly sure there's any absolute best or perfect setting, as it always comes down to us. Our ears. Our preffs... and with the gear on hand at the time.
Use the one you enjoy most.
As for the PURE or DIRECT setting, with all my recievers present and past, and processors too, those selections dismiss completely any ancilary tone or upsampling preferences... defaulting to the current formats word length and sampling rates, and eliminating any equalization, tone controls, or LFE output... hence no sub. Just pure unadulterated unconfigured and simple signal pass thru... this can be either good or not so good, depending on the current gear or listening prefferences.