I'm not sure if anybody is interested in this, but it seems that the workaround I detailed above lets me use Basilisk II without too many problems (you just have to remember to use it). Let me explain a little bit more about how to do it. It's probably easist to understand what the problem is by imagining the Mac desktop. If the Mac's cursor is on the bottom lefthand side of the desktop and you tap the screen at the top right, it will draw a selection rectangle on the desktop, just as if you had dragged the cursor instead of just tapped it. That is a pretty big problem, since it means that if you select an item, you can't unselect it easily and you may end up moving it accidentally. And it also makes selecting checkboxes almost impossible, since they will be clicked again when you tap someplace else on the screen.
The Fn key solution works like this: any time you know that you will want to move the mouse without dragging, you must hold down Fn. So if you have a folder selected and you want to unselect it, you need to hold down Fn and tap someplace else on the screen to first move the cursor, then tap again to unselect it. I basically just do this any time I want to move the cursor. It turns clicking on anything on the screen into a two-step process (hold Fn and move cursor to desired position on screen, release Fn and tap) but at least it works. Before, I was unable to do a lot of basic things because of this problem.
I did some more experimenting with Mac software, now that I can control it reliably. One thing I can say is, make sure you select the proper CPU in the Basilisk II settings. It must match the one from the ROM you are using or programs won't work properly. At first I had the wrong CPU selected, and while the OS and many programs seemed to work, I got some strange errors with some programs. Choosing the right CPU solved this.
I had a disc for Photoshop 4 lying around from my first Mac, so I installed that via the PC version of Basilisk II and then transferred the hard disk image to the Zaurus. At first Photoshop wouldn't load, and I thought it was because of some incompatibility with the Zaurus version of Basilisk II (it said the monitor settings were invalid") but selecting the proper CPU in the preferences solved that. Photoshop takes maybe a minute and a half to start up, and it's pretty slow to use as well, but you might be able to get some simple things done if you were patient. Actually, it didn't seem that much slower than the Gimp when I tried it in XQT. It's pretty cool to see Photoshop running on the Z. I wish I had a copy of Word 5 for the Mac. That might actually be pretty usable in emulation.
Anyway, I'd still be interested if anybody could come up with a better solution than this for the mouse problem, but at least I can use Mac applications now.
