Using the commands rate-limit attribute and rate-limit vendor wont change/add the [shaper] section in the pppoe.conf file. Adding the shapper parameters manually works fine.
Ex:
vyos@vyos# set service pppoe-server authentication radius rate-limit attribute XXXXX
vyos@vyos# set service pppoe-server authentication radius rate-limit vendor XXXXX
I checked the latest rolling and I can see shaper vendor attributes
set service pppoe-server access-concentrator 'R1'
set service pppoe-server authentication mode 'radius'
set service pppoe-server authentication radius dynamic-author key 'fdsfsdfsdf'
set service pppoe-server authentication radius dynamic-author port '3838'
set service pppoe-server authentication radius dynamic-author server '100.64.0.2'
set service pppoe-server authentication radius nas-identifier 'R1'
set service pppoe-server authentication radius nas-ip-address '100.64.0.1'
set service pppoe-server authentication radius rate-limit attribute 'Cisco-AVPair'
set service pppoe-server authentication radius rate-limit enable
set service pppoe-server authentication radius rate-limit vendor 'Cisco'
set service pppoe-server authentication radius server 100.64.0.2 key 'FOO'
set service pppoe-server authentication radius server 100.64.0.3 key 'FOO1'
set service pppoe-server gateway-address '100.64.0.1'
set service pppoe-server interface eth1