Well, later, when I started installing some of the custom scripts available here, the ones that were made to work in the Tools palette showed up in an "Other" group at the bottom, as others here have also experienced.
Some time later, I had made a modification to the code of one of the tools, and had backed up the original tool script by renaming it. Afterward, I noticed that there was an extra tool in my palette with no icon. Hovering over it showed it to be the renamed tool, and this gave me a little more insight into how AS handles the Tools palette.
I think it was Vern who mentioned once that he had "replaced" the original Lost Marble tools with Fazek's modified versions, and I didn't know if that meant that he had renamed Fazek's tools to the corresponding names of the original tools and deleted the originals, or if he used the method I'll describe here: I experimented in the _tool_list.txt file by changing the entries in the original sections (Draw, Fill, and Bone) to refer to Fazek's tools instead of the originals. When I did this, Fazek's tools were at the top, and the original tools were now relegated to the "Other" group. So from there I made new entries throughout the file wherever I decided the other new scripts belonged, and moved the originals out of the folder entirely, so there was no longer any "Other" group. Tools only appear in the "Other" group if they're not explicitly placed somewhere in the _tool_list.txt file.
Finally, there were a couple of tools that didn't really fit in any of the existing groups, and so I tried another little experiment, duplicating a section of code from the _tool_list.txt file that delineated a group, and named it "Keyframes". Voilà, a new group appeared in the palette, and that's where I put the 4 keyframe-based tools you can see in my sample image.
So that's how to organise and clean up your palette, and if any of it was unclear, here's a link to my _tool_list.txt file for you to look through.
