The closest thing I can think of to a legitimate case for something like the "book two hotels" scenario would be a situation where you'd be at the same hotel for two significant blocks of time (say, two four-day weekends) but would be somewhere else in the middle. In a situation like that, if the period in the middle is only a night or two, there are two things that kick in:
(1) You might be able to get a good long-stay rate for the 10-11 nights that doesn't apply to shorter stays. I've seen some extended-stay rates that require 4-5 nights on occasion.
(2) If you want to "base" some of your luggage at one location and only take a smaller bag with you (rather than loading everything into either a rental car or dealing with checking it), that can also play a role.

The first factor can lead to the through-reservation actually saving money if only one night is involved (if the extended-stay rate is $10/night less, for example, that plus taxes could offset the cost entirely and then some on two longer stays). The second...well, depending on your airline situation, etc., there's the possibility of either paying for the convenience or saving on bag fees.

To lay out a scenario for the above, and inverting the schedule a bit (with the first-person pronouns being generic in nature here), let's say that I'm in LA for two weeks on a business trip or assignment. My employer doesn't really want to pay for two round-trip flights and I agree (I live on the East Coast, so a one-way trip is either an unpleasant red-eye or a shot day). However, I'd like to go to San Diego over the weekend and I don't particularly feel like hauling all of my stuff onto the Surfliner (or I want to go to the Bay Area but don't want to deal with dragging it all to/from the airport) and besides, I don't need my suit for what is basically a weekend getaway.

(I actually had a situation like this last year, where I got pulled off to West Palm for one night, and I think I ended up at a Comfort Inn or a local off-brand on one end of things and a Marriott-family hotel on the other.)

The way to cut through this is, most easily, to just throw the weekend onto another chain (e.g. Hyatt). But this is the sort of screwy situation that these rules don't really handle well, since in a sense you are occupying both rooms in a sense.