When i ran my test and mounted the boot environment file my home dirs and data were all there.. are you sure on this?
Keep in mind that if you simply "restore" a boot environment on the same machine you made it from, regardless from where it came from (in this instance a compressed file) the dataset that the home directory's are in, are still in the zfs pool if we are talking about the same machine without a reinstall. Therefore, it will show up.
But lets say you had a disk failure, and needed to to restore to a new disk. Once you reinstall FreeBSD from image, then import the pool from the file that you exported, and saved to a different location, the home directory will be empty. This is because boot environments do not include that dataset. This is due because 1). your export file could become huge. 2). you would have to restore the entire boot environment just to get at a single file in your home directory, etc.
In the situation that is being discussed in this thread, You are trying to save the system state, as it were, so that is all boot environments do (base system and pkgs that have been installed).
It seems as the configuration that you are alluding to is also possibly a desktop environment and you want to preserve your customizations? These configurations typically live in your home folder and typically configurations to the base system rarely live here, and therefore are not considered for the boot environment, either.
This is why you should also have a separate backup of your home directory. Use tar and .xz to compress and archive the home directory(ies) so they can then be placed after the system has been "restored". Or utilize zfs to send the home directories to a file just a
cracauer@ suggested. But then again you can't just grab a single file out of it.
If you have a spare machine or a system powerful enough to run virtualization, test run this so you can experience first hand what it will do.
Learning to backup a system and your data is very important. Many people stop there, and then struggle to restore it. Learn how to backup, but also learn how to restore it as well. Nothing worse learning to do it under the gun.
jda