I wouldn't say "evil". Often these tools are made with the best intentions. However, we've seen them do stuff that isn't recommended and has caused issues.
For example, one of the options in the past (and it might still be there) is an option for Fire TV users to pre-install a keymap, but without a description for what it does. This keymap added audio amplification as a way to control the volume, since the Fire TV doesn't respond to software volume control. This can work, but the way audio amplification works will cause distortions and not actually turn anything "down".
Another example, the "zero cache" option is one of the most used in these maintenance tools, but there's no warning for users that have low internal memory. Fire TVs and other Android devices with 8 GB or less will crash or have orphaned temp cache files that don't clear out, causing playback issues or running out of internal memory. It bypasses the entire reason we don't add such settings to the GUI, because they can't be safely turned on for all users.
(side note, the buffer rate seems to be one of the safe cache-related settings, and in v15 it has been increased by default, fixing a lot of issues without requiring any advancedsettings.xml files)
Then there's other totally pointless options, like "erase logs". Logs are automatically erased every time Kodi is restarted. The current Kodi session uses kodi.log, then when restarted kodi.log will become kodi.old.log, and the previous kodi.old.log gets deleted. The only time I can think of (other than hiding porn) for when one would ever want to manually delete the log would be if something went horribly wrong and the log became huge, and in that case the user will probably want to keep the log in order to report that very issue.
Same with "purge packages" being useless. Packages are the add-on packages for add-on rollback (a little known feature in Kodi that allows you to rollback to a previous version of an add-on, incase an update breaks something). Packages are automatically purged so that only 200 MB of the most recent add-on versions are saved, and that 200 MB size can be further adjusted all the way down to zero via
advancedsettings.xml (wiki). At 200 MB there really isn't any significant savings to even bother manually purging or trying to make the saved size smaller.
Even more useless are options like "add-on remover", "skin remover", and "repo remover", which are built-in functions of Kodi in the first place. You can do all of that more easily without using any extra maintenance tool add-on.
Things like the "config wizard" have been found to install spam-like services. For example, a pre-configured twitter add-on that beeps you whenever some group like tvaddons wants to tell you something, even while watching a video. That specific example caused a flood of users getting a persistent error message about a bad search, and users had no way of knowing how to disable this. Another example, that horribly tacky background picture with their logo all spewed on it.
I don't know if they still do this, but they used to modify the files of other add-ons, which made undoing what the maintenance and configure tools did almost impossible without totally redoing the install from scratch.
Nothing "life or death", for sure, but using these tools obscure issues, sometimes cause issues, and generally make it harder to provide support for our own users. This has caused us to become very frustrated with those tools, when they would otherwise be a welcome addition to the community. We've even tried to provide advice on how different things could be improved, and most of that has fallen on deaf ears.