In this case tho bom can not be created from within eeschema. The information about where the component is located is only known by pcb_new.
But pcb_new does not know about costom fields added to the symbol in eeschema.
Ideally the bom tool is located outside of eeschema and pcb_new. It would use the data from both plus maybe from a material database to create a bom. (But i don't think anyone will implement something like that in the near future. There are much more pressing issues like the new symbol library format.)
Maybe as a first step it would be possible to get the layer as an output of the bom generated in pcb_new. Then one could write a relatively simple script that combines the output of eeschema with the output of pcb new.
But to get this you might need to talk to the developers over at the bugtracker. (create a bug marked as wishlist) Not a lot of developers visit this forum regularly.
Also have a look at this tool by @pwuertz. Your original question sounds like you want to have some support for hand assembly: