Well, we don't know for sure it's the same as 960H. So I'll answer based on what I've seen in our 960H tests.
1. The megapixel sensors do seem to make a difference in image quality. I believe in order to take advantage of it, though, you need a cleaner digital/analog conversion in the DVR. This is why "normal" D1 DVRs don't see much of an improvement from high TVL cameras.
2. All ports on these DVRs are 960H (or 1280H). It's simply the capture resolution that's set. You can change them to D1 or QCIF or 960H, as we did in our analog vs. IP testing.
960H and presumably 1280H is a capture format, not a transmission format. NTSC is NTSC is NTSC. But once that video hits the capture card it can be captured at whatever resolution you want, including 1280x480. You could record it at 16MP if you want. It's just questionable benefit. That's what's really strange here. We've seen practical benefits to high TVL cameras, and the quality is quite a bit better than standard 450-600TVL models. So capturing it at a resolution above D1 may have some benefit...but why they choose to stretch this good quality video, we do not understand.
3. Are you talking about loop-thru inputs? Typically the DVRs we've seen haven't included them at all. I think since analog has shifted downmarket, people aren't expecting them near as much as they used to, so manufacturers are removing them to save a few dollars on the recorder. The 960H DVRs we have have none, but do have a couple spot monitor outputs.