When should I use a PersistentDict, and when should I use a Folder? What is the difference between them in terms of updates, internal structure, performance, etc?
A PersistentMapping is simply a implementation of the python dict type (via the standard library UserDict base class) adjusted for the Persistence semantics of the ZODB; it saves from having to set the _p_changed flag on the nearest class that inherits from Persistent every time you alter the mapping.
A Folder is a much richer type, implementing events, integration with the Zope web interface (ZMI), through-the-web arbitrary properties (attributes with type validation), management of Zope permissions, validation of sub-item ids, import/export, etc. Sub-items folders are stored as attributes on the object itself, with some metadata stored in a private dict on the instance.
Use a Folder when you need any of those extra services (delegation of permissions, id validation, etc), use a PersistentMapping otherwise. Performance wise looking up or storing items is not going to differ much; one is a straight python dict underneath, the other is the instance __dict__ storing the items.
If you are looking for conflict avoidance, you should look into BTrees, the OOBTree class is basically a persistent mapping where values are stored in persistent buckets, avoiding collisions in most cases, and providing conflict resolution for the rest.
If you want Folder semantics with BTree storage semantics, look at Products.BTreeFolder2, and add-on that implements the Folder interfaces but stores sub-objects in a OOBTree instead of as attributes directly on the instances.