A little extra pertinent info here. When Tinderbox expects one match and gets more than one match, it selects the first match by $OutlineOrder. Thus faced with this ambiguity:
…the result is as @eastgate describes., though I figure a picture will help some others reading this.
The $Path of both the separator and the actual template containers is the same
/Templates. Remember that a separator is a note, just one shown in a special manner.
Given their very special purpose it is a good idea for both the Prototypes and Templates folder to leave them where they are and not use that $Name anywhere else. For the same reason of potential name classes it is also a good idea to make sure the title ($Name) of any individual prototype or template is also unique. That is why you will see many users adopt a practice of using a prefix letter or character (asterisk, underscore, etc.) at the start of the name. This has two useful effects. It reminds the user this note has a special purpose and it won’t get into a nameing collision as has occurred above.