Here’s a patch for ppp which allows to change NAS-Port-Id behavior. It adds a new option for ppp.conf:
set rad_port_id [default|pid|ifnum|tunnum]

default means the default behavior (i.e. the way that ppp works now)
pid means NAS-Port-Id will be an ID of the process owning the corresponding interface
ifnum means NAS-Port-Id will be an interface number (i.e. stuff that if_nametoindex() returns)
tunnum like previous, but a tunnel number.

Here’s a first version of the patch. I have tested it in combination with poptop and freeradius.

I wonder if it worth submitting a PR…