Term not being migrated into taxonomy reference field
I'm sorry that in 8 months no one has answered this question.
I was stuck on this as well and finally got it to work by using the following format nested under the process key of your migration that will look up the previously migrated taxonomy:
field_taxonomy_term:
  plugin: migrate_lookup
  migration: migrate_taxonomy_terms_en
  source: field_taxonomy_term

The field_taxonomy_term from your node source should be the entity id of the taxonomy term.
Also it should be noted that I migrated the taxonomy vocabulary and the node that will reference the taxonomy as a group.  I'm not sure if that matters or not.  The order the migrations are executed in is determined by setting the dependency on the taxonomy migration in the node migration.