TiddlyWiki itself prefers to store settings in tiddlers. Every setting has its own tiddler. This is good and bad.
One other option is using a JSON tiddler to have all settings in one place. For example, the Shiraz plugin uses a JSON to store its settings.
Settings / Configurations here are: hide/show a toolbar button, a page control, activate conditionally a stylesheet, a viewtemplate, etc.
One may create a ViwTemplate for such config tiddlers to produce a user friendly UI for interactive configuration.
What is your way to configure your tools in TiddlyWiki?