tax_query on base query, causes template confusion

I understand what I am doing is weird. But I know I am not the only person out there doing this. I also should add that this was not a problem until WordPress 4.2.

We use pre_get_posts hook to filter what is shown on the base query, using a custom taxonomy. This allows us to direct users to different subdomains and show alternate posts per subdomain. Recently I created a custom post type for a plugin, it also shares this base query custom taxonomy rule and one for its own purposes. This way I can filter by ‘area’ then by ‘category’.

When I navigate to a term in the new custom taxonomy of the custom post type on the front end, I see the correct filtered output. The posts I am expecting to see. However the meta in the template head, and the template itself, is showing as if it were from the taxonomy applied to the base query. I am quite confused.

It is as if the template is basing itself on the tax_query, but the post output is the correctly filtered output. Has anyone bumped into this before? What I want is for it to correctly show the template for the taxonomy I am viewing, not the tax_query.

array (size=66)
  'bw_category' => string 'uncategorized' (length=13)
  'error' => string '' (length=0)
  'm' => string '' (length=0)
  'p' => int 0
  'post_parent' => string '' (length=0)
  'subpost' => string '' (length=0)
  'subpost_id' => string '' (length=0)
  'attachment' => string '' (length=0)
  'attachment_id' => int 0
  'name' => string '' (length=0)
  'static' => string '' (length=0)
  'pagename' => string '' (length=0)
  'page_id' => int 0
  'second' => string '' (length=0)
  'minute' => string '' (length=0)
  'hour' => string '' (length=0)
  'day' => int 0
  'monthnum' => int 0
  'year' => int 0
  'w' => int 0
  'category_name' => string '' (length=0)
  'tag' => string '' (length=0)
  'cat' => string '' (length=0)
  'tag_id' => string '' (length=0)
  'author' => string '' (length=0)
  'author_name' => string '' (length=0)
  'feed' => string '' (length=0)
  'tb' => string '' (length=0)
  'paged' => int 0
  'comments_popup' => string '' (length=0)
  'meta_key' => string '' (length=0)
  'meta_value' => string '' (length=0)
  'preview' => string '' (length=0)
  's' => string '' (length=0)
  'sentence' => string '' (length=0)
  'fields' => string '' (length=0)
  'menu_order' => string '' (length=0)
  'category__in' =>
    array (size=0)
      empty
  'category__not_in' =>
    array (size=0)
      empty
  'category__and' =>
    array (size=0)
      empty
  'post__in' =>
    array (size=0)
      empty
  'post__not_in' =>
    array (size=0)
      empty
  'tag__in' =>
    array (size=0)
      empty
  'tag__not_in' =>
    array (size=0)
      empty
  'tag__and' =>
    array (size=0)
      empty
  'tag_slug__in' =>
    array (size=0)
      empty
  'tag_slug__and' =>
    array (size=0)
      empty
  'post_parent__in' =>
    array (size=0)
      empty
  'post_parent__not_in' =>
    array (size=0)
      empty
  'author__in' =>
    array (size=0)
      empty
  'author__not_in' =>
    array (size=0)
      empty
  'meta_query' =>
    array (size=0)
      empty
  'tax_query' =>
    array (size=2)
      'relation' => string 'AND' (length=3)
      0 =>
        array (size=5)
          'taxonomy' => string 'n_area' (length=9)
          'field' => string 'slug' (length=4)
          'include_children' => boolean false
          'terms' =>
            array (size=2)
              ...
          'operator' => string 'IN' (length=2)
  'ignore_sticky_posts' => boolean false
  'suppress_filters' => boolean false
  'cache_results' => boolean true
  'update_post_term_cache' => boolean true
  'update_post_meta_cache' => boolean true
  'post_type' => string '' (length=0)
  'posts_per_page' => int 10
  'nopaging' => boolean false
  'comments_per_page' => string '200' (length=3)
  'no_found_rows' => boolean false
  'taxonomy' => string 'bw_category' (length=18)
  'term' => string 'uncategorized' (length=13)
  'order' => string 'DESC' (length=4)