They do a lot of research at Baylor and perhaps that is part of the protocol in order to learn how to compare a complete clinical (nothing palpable) response/complete radiologic response (nothing on mammo,ultrasound or MRI) with a complete pathological response, which they can only tell under the microscope and only if they are sure they got the whole area which might have tumor cells.
More thinking out loud/speculation:
To remove the whole 5 cm with a >2mm or more normal margin all the way around (what they normally aim for I believe)they might believe that they would have to make a very disfiguring lumpectomy. Since they no longer know exactly where the tumor was, just its general location within the quadrant of the breast, they might need to remove more to be sure to removed where it might have been. I don't know if your mother had particularly large breasts
but that is a lot of breast tissue to remove and still leave something aesthetically acceptable to your mom. Some surgeons (especially male ones, I believe) tend to make the judgement for the patient and only present one option believing they are in more of a position than the patient to decide what procedure to have--not based on whether the tumor may come back but what the result might look like, how it may be reconstructed etc. I think it reasonable that your mom not agree to anything until she is told of all the alternatives and the pros and cons of each. They may tell you it is too close to the skin, that they hope to avoid radiation therapy (there has been controversy in the past as to whether to radiate after mastectomy--don't know the current thinking in cases with such a good response to neoadjuvant therapy)
Some surgeons have been known to think that their handiwork will be changed (shrinkage, discoloration, hardening) by radiation therapy so why not do a mastectomy, try to avoid radiation therapy and then reconstruct?
It sounds from your post, that when asked, the surgeon is willing to go either way, lumpectomy vs mastectomy--has he/she talked with the oncologist and gotten their reasons for recommending the mastectomy.
The consensus on what constitutes the best surgical treatment of breast cancer treatment is also changing all the time--just as the oncologic and radiation therapy treatments are undergoing change.
You might go into search and look up my link to the Miami Breast Cancer Conference videos a few weeks ago (I recommended several within the past 3 wks or so). I did not have time to listen to all the talks on surgical treatment, but I bet there is a lot of information there.The linke:
http://www.cancerconf.com/media/2008/wednesday.php
click on the different days of the week and peruse the different talks on surgical treatment
Hope this helps