All Tinderbox level preferences are used as the defaults for any new TBX document and become the default values for those preferences at document level unless subsequently altered, in which case the document's preference value is used.
The window is titled "Tinderbox Preferences (for new documents)".
The Tinderbox preferences can be accessed several ways:
There is just one preference that exists only at app level (in the General section). Conversely, there a number of groups of settings that are available only at Document Preferences level: Ping, Weblogs, Mail and Simplenote. This is because the latter are usually document specific - either because they will be used only in some documents or the settings may need to differ from document to document.
For all preference tabs except 'Ping' there is no way to reset factory defaults, so it is advisable not to tinker with settings until you have gained some experience with Tinderbox. Experiment by changing preferences at (per) document level until you are sure you want to apply the change to all files; note that file configuration changes only affect new files, whereas display settings tend to apply to all files. If all else fails you can reset your Preferences.
Resetting text-based link colour is a notable exception as the link colour values are embedded in each individual link at time of creation and can only be altered subsequently by removing and recreating the link or by editing the raw XML outside Tinderbox (backup first if doing so!).