Yeah, to elaborate a bit, Straight simply turns off Yamaha's effects processing (the extra DSP modes). The YPAO settings are still in effect, as is the bass management you have selected. So, Straight mode is good if you depend upon your subwoofer for decent bass for music.
Pure Direct turns off more things - the YPAO settings (and manual setup menu settings) are disabled, so there is no bass management, speaker level balancing, etc. Therefore no sound from the subwoofer. The tone controls are also bypassed, video switching is turned off, and the display powers down.
But Pure Direct isn't just for analog sources. It still works for digital sources, but only 2-channel digital PCM. So, if you have a digital link from your DVD/CD player, and are playing a regular CD, the two-channel PCM will still be decoded by the receiver, and play in Pure Direct mode. If you feed it a multi-channel digital source, however (Dolby Digital or DTS), it will try to revert to the corresponding analog inputs (just the front channels). There is a warning about playing DTS-encoded CDs, which will just make noise. Bottom line is that it is just for 2-channel stereo, but the source could be digital PCM or 2-ch. analog.
In my set-up, I have two-ch. analog outputs from my DVD/CD player fed to the CD input of the receiver, and a digital link from the DVD/CD player fed to the DVD optical input of the receiver.
If I have a CD playing, I can use Pure Direct in analog form by selecting the CD input, or use Pure Direct in digital PCM mode by selecting the DVD input. I usually use the latter, as the PCM decoders of the receiver are newer than those built into my DVD/CD player. But, I sometimes use the analog path if the CD I'm playing supports HDCD, since my player decodes HDCD, while my receiver does not. In any case, the sonic differences seem minimal between the two versions of Pure Direct, and may even be imaginary! I AM convinced, however, that Pure Direct (done either way) sounds better to my ears than Straight 2-ch. stereo. I also think the little blue light is awful purty!