Interresting question, but as I looked for more details, I did not found relevant information about the rules beyond this.
Looking for a better explanation, I will give my opinion about this.
The rule expected for the use of en and y, in this case, is that those words replace the attribute of the verb, to avoid redundancy. Therefore “Elle met du temps” becomes “Elle en met”. The extreme case, if you did not mention “du temps” earlier: “Elle en met, du temps” in which the comma denotes a true separation between “Elle en met” and “du temps” as two clauses.
As a native speaker, I also say “elle en met du temps” and moreover “Elle en met du temps à rentrer du travail”. I guess that en refers to temps and is intended to replace it. But “un temps” or “du temps” still remains, so I guess “en mettre un temps” is another pleonasm in our language, such as “Au jour d'aujourd'hui” or “Incessament sous peu”. Pleonasm is a way to emphasize a part of the sentence (such as “Au jour d'aujourd'hui”, which underlines the current date of the fact), so “Elle en met un temps” might emphasize the extreme duration (or our impatience). But it also often disappoints your listener as it denotes a misunderstanding of the language: use it carefully :).
Edit : 'Elle en passe du temps'
"Passer du temps" and "mettre du temps" may not be used in the same context.
"Mettre du temps" describes the time it costs to execute an action.
"Passer du temps" describes the business involved in your spare time (gardening, playing, etc).
There's another verb : 'prendre'. 'Prendre du temps' means almost the same as 'mettre du temps'