Custom Fields not emailing
The fact that you are seeing Primary suggests this has been added as an Address custom field, and it seems that these new-ish field types have not been fully integrated to receipting.

You have some options

1/ change your field to a standard Contact field and then edit your tpls to have the field show where you want it (this seems the 'right' way to fix this since otherwise you are using an Address field, with its options of Location Types, for a field that should not be offering Location Types)

2/ get the code improved so these fields do show in the receipts either by contributing a patch or funding a Partner to do this on your behalf and help grow this open source project.