You make a good point and raise some interesting questions. However, I think eBay sees the new on-time delivery "Question" and the "Shipping Time DSR" as distinct questions. The problem is, in my opinion, I don't think buyers will always see them as distinct.
The new on-time shipping question is intended to judge whether the delivery time frame has been met, whereas the shipping time DSR was intended to ask the buyer whether the seller dispatched the item promptly. These are two completely different factors, but it's easy for buyers to get them muddled.
Buyers often equate the DSR rating for "Did the seller ship quickly" to mean "Did you get your item promptly". (For some reason I can't grasp, eBay never saw fit to change the DSR wording to make it clear that the seller was being judged for quick dispatch). So in such instances, if a buyer answers "Yes" to the on-time question, one would assume they would be likely to also give a 4 or 5 star DSR for shipping. In other words, happy on both accounts because they think they're essentially being asked the same question twice.
On the other hand, a buyer who does understand the distinction (or is confused about what is being asked) could feel that the seller was slow in getting the parcel out the door, even if it did arrive within eBay's stated delivery window. As you say, that buyer might be inclined to answer "Yes" to the on-time question, but leave, say a 2 or 3 DSR for shipping. Since eBay is now telling us to lengthen our handling time to "pad" the delivery estimates for our own protection, this could conceivably affect buyers' responses to that DSR if they look at the listing to judge dispatch time (even if the seller is actually dispatching sooner).
One thing to keep in mind is that the DSR for shipping time will no longer impact seller performance rating, so that DSR (and the other DSRs) will be displayed only for informational purposes to buyers. Still, it has never worked properly as a fair evaluation of sellers' dispatch performance, and now it appears it's virtually redundant, so I think it should be dropped completely.
To say the least, it will be interesting (some might say frightening) to see how this plays out once we sellers start to get the numbers coming in on the new "Question". Since performance in this regard is being measured on such a narrow statistical base, every single response to the on-time Question will be absolutely critical for smaller sellers.
