Some quick notes on the bugs you found:
The “missing //@ prefix” bug is #600578, fixed in upstream, in sid and in squeeze. Thanks :-)
The “boot partition stays in /target/boot in final install” bug is not in BTS. It was present in a preliminar version of partman-zfs which was never uploaded. The version currently in the archive correctly uses “altroot” option to fix this.
The “/lib/modules is needed for boot” problem was reported as #600568, but I haven’t been able to persuade the kFreeBSD maintainers that this is necessary. It’s not critical anyway.
Glad you finally got a working setup.