[eschwartz]

1. No. Metadata is updated at the following times:
   • Conversion. All current library metadata is embedded into the converted book. Metadata embedded in the conversion source ebook is totally ignored.
   • Embed Metadata and Polish book. All metadata that can be updated will be embedded into the library copies. (You can choose to restrict this to specific formats.) Certain types of metadata are not supported by certain formats -- notably, only EPUB and AZW3 support updating covers.
   • Send to device, Send to email, and Save to disk. ^^Ditto for the exported books, except plugboards, if configured, are applied.
   • Edit E-Book by default updates books when saving, following the same rules as Embed Metatdata/Polish book. But most people don't ever use this anyway.
2. Identifiers, like any other metadata, are derived from the library metadata. The only exception I can think of is mobi-asin, which is derived from a mobi header. That header can be set from the amazon|asin|mobi-asin identifier using the Quality Check plugin, which can be useful for things like goodreads/store linking on-device.
3. See #1