Taxonomy Term Reference Fields Don't Get Created on Nodes During Migration
The problem wasn't in migrate_plus.migration.upgrade_d6_field_instance.yml but instead the problems were in  migrate_plus.migration.upgrade_d6_field.ym and migrate_plus.migration.upgrade_d6_field_instance_widget_settings.yml.  Also in the term yml files I had to update the field name to include field_ in the file name.

I documented how I was debugging and what I was changing here.