This is not kind of question for SO, at least in most parts. However:
1.) TBO and SBO are just architectural approaches for specific requirements. If you have specific code that you want to run for objects of specific type and not only for objects of subtypes, than you need to change object model to apply logic for all objects in type hierarchy. This isn't a problem with Documentum object/type model.
For example: You have custom_document as subtype of dm_document and custom_child1_document and custom_child2_document, both subtypes of custom_document. You have TBO set to custom_child2_document.
You don't want to apply SBO to have custom logic available everything under dm_document.
Just add TBO to type custom_documentm and you'll have your logic for all types under dm_document.
2.) You cannot call behavior class without invoking component. If you have specific code you want run from other places, isolate it at some other place and run it at will.
3.) You don't need to specify scope for your WDK configuration. However, once you learn WDK in details you will find it useful.
4.) Folder is object. You need to know that when you access objects via folders you need access permission for both folder and document linked to that folder (Read level is enough). You need only permissions on object id you access that object from DQL for instance. Basic and extended permissions are meant to be used in specific cases, you don't need extended permissions to read object content if you have Read basic permission on your object. However you need Relate basic permission + Run procedure extended permsission on target Workflow to start workflow with that specific object as attachment/package. Different rules go when you want to add object inside specific folder. But this is long story.
Regarding folder security - check this article.
