Hi Danielle,
1. Many of the modifying operations in JSTS does not support Z which is limitation of scope from upstream - see
https://locationtech.github.io/jts/jts-faq.html#B4. There is no plans to extend the scope in upstream AFAIK and this means full Z support also out of scope for JSTS.
2. A WKB parser/encoder would be a welcome addition. It (and other I/O related classes) could not be translated from the upstream Java source.
3. I don't think it's intentional and could probably be considered a bug.
Regards,
Björn