hook_theme_suggestions_HOOK vs. hook_theme_suggestions_HOOK_alter
The linked module should try to add suggestions in hook_theme_suggestions_HOOK as long as it doesn't depend itself on existing suggestions, so that other modules still have the option to override these suggestions in an alter hook.

Hooks don't have priorities, which having two hooks, one main and one alter hook, is trying to compensate. This is like a priority system with only two levels. If you add something on the second level there is no third level for other modules, unless they resort to unusual solutions like module weights.