I guess you mean you import the items from a exported job build right?
In this case it is clear because the exported job does not carry the items from the meta data section. A job always knows all values it needs and has a reference to the metadata elements. If this reference cannot be found the job declares the variables or schemas as build-in.
The option "with dependencies" is an option available in the Item Export not in the Build Job function.
If you export a build job and include here the sources I am pretty sure the meta data are not included. If you import these items in a separate repository - obviously the schemas and context variables have to change to build-in.
You question b is not clear for me. In the studio you can export a standalone job and I thought you already did that.
If you mean how to build a job without the studio - sorry this is not possible yet. In the enterprise edition you can export a Build Job with Ant or Maven scripts included to build the job from the exported Java source code for the job.