After reading your post, I decided it was time to see if there would be any problems running my utilities on my OSX partition.
I have a G4/466/512MB RAM. I have the original IBM 30GB HD plus a Maxtor 40GB HD...I have the three partitions on the IBM and four partitions on the Maxtor. I am using a partition on the Maxtor for OSX.1 and another partition on the Maxtor for OS 9.2.1 ( this is also the one selected for Classic).
I have all my utilities on the Classic partition...so I booted from it and started with Norton's Disk Doctor(6.0) and checked the OSX partition...all okay. Then I checked the directory with DiskWarrior(2.1) and it was 36% fragmented...so I rebuilt the directory. Then I used PlusOptimizer(1.3) and defragmented the OSX partition...other than a few items it could not move such as the directory and some invisible files, every thing went smoothly.
I then used TechTool Lite 3.0.1 and rebuilt the OSX desktop.
To check it out, I booted from OSX, connected to MacOSX.com and am answering your post. No problems that I can tell.