This is a fascinating question, and one that has been debated since my student days (though interestingly, some of what was considered obscure when I first started auditioning, is now quite standard!!)
Here are the two opposing arguments:
Arguing for less known rep in an audition:
You will not be compared to well known singers who sing the particular arias you are doing; you will show musical, vocal, and linguistic range and skill; you will knock the cobwebs out of the ears of your auditioners who have listened to fifty Deh vieni non tardars that day.
Arguing against less known rep in audition:
What are you hiding? (this is the classic - your choice is based on trying to cover up a vocal, musical, dramatic, or linguistic deficiency; you will be perceived as not being grounded in the core rep of the operatic tradition; some less well versed auditioners will not have a point of reference for your performance, thus weakening your chances;
As with many things about auditioning, the answer is individual, but a couple of suggestions (based purely on my own biases, and those of some colleagues I've spoken with):
1. Mix it up - If you want to do a number from a fairly obscure work, pair it with something better known, so that you can show your "chops" on the standard canvas.
2. If you have audition rep that is more obscure, have an accompanying resume that explains that - in other words, if you have a number of credits doing off the beaten path rep, your audition choices will make sense.
3. Make sure that you are not choosing this rep to cover a weakness - make sure that it is a proactive choice.
4. Vett it - with colleagues, coaches and other professionals you respect - don't rely purely on your own judgement for this one!