There's simply no evidence that Walmart is a drag on wages compared to retailers it replaces. Quite the opposite actually.
Furthermore, just because the paper is on NBER, it doesn't mean the organization did the research. It's just the organization that hosts the paper. If you click through, you can see that the work was done by faculty at Stanford and The University of Michigan.
http://www.nofrackingway.us/2012/11/01/shale-boom-nber-conse...
http://www.cnbc.com/2016/06/03/walmart-can-afford-15-minimum...
The paper cited is a typical right-wing conservative position that corporate ladders with management positions provide workers with more opportunities for advancement, and thus possibly higher wages.
>...The NBER is the largest economics research organization in the United States.[2] Many of the American winners of the Nobel Memorial Prize in Economic Sciences were NBER Research Associates.
https://en.wikipedia.org/wiki/National_Bureau_of_Economic_Re...
"Research" can be used to defend any argument in this debate.
The NBER has 3-4 sources of funding and consistently reinforces conservative, monopolistic positions.
Mom and pops very rarely have good benefits because they don't have the resources that larger firms have. It's complicated and expensive to set up things like health care plans and 401Ks. This is why the ACA employer mandate doesn't apply to firms with fewer than 50 employees.