Well, I think I finally got it right. First off, thanks to red99 for all the good ideas!
I decided that I really needed to analyze the problem a bit more logically, so I spent some time with the wiring diagrams and poking around the car to see how things really worked. It turns out that there are indeed two terminals on the latch microswitch, one for the trunk light and one for the instrument cluster (red99, I think you may have been looking at the diagram for the non-power lock models). The contacts are closed (short to ground) when the hatch is open. I disconnected the connector from the switch (easily accessible when hatch trim is removed) and manually shorted each connection to ground - they worked correctly (trunk light and warning light came on), so nothing wrong with the wiring. Must be the switch, I thought. Turns out the switch is like $60-80, so I decided to explore further before laying out bucks and removed the latch assembly for bench testing (requires 10 mm triple-square/12-point bit).
After playing around a bit, I found that when closing the latch, the switch opens the trunk light circuit first, then the warning light circuit after moving a little further (probably why it's not so cheap). This corresponds to two positions of the latch hook, when it first captures the fixed body part of the latch and then when it snaps around that part to pull the hatch down tight. So something was preventing this second operation from occurring.
To make a long story slightly shorter, I apparently had adjusted the fixed part of the latch too far down, preventing it from tripping the latch hook properly. After some trial and error I now have it where the lid latches completely with a firm (but not too firm) slam. It actually needed to be a little cockeyed, with one end higher than the other. Amazingly, it ended up pretty close to where it was before I replaced the trunk seal. Imagine that!
I haven't driven it on the freeway yet, so the last thing will be to see if the road noise is gone and no rattles were introduced.