The warehouse staff are often not musicians. In the summer especially, they hire temps. I've seen many issues with beginner packages and rentals that were from people not paying attention to detail or just not knowing. Small vs large shank mouthpieces, tenor sax mouthpieces or ligatures in alto saxes. A couple times I've seen the old purple Essential Elements book instead of the yellow EE2000. Tradition vs Standard of Excellence. A good rep will double-check your delivery before bringing it out, and be quick to fix problems that do occur.
As someone else said, M&A uses the Musician's Friend warehouse. That means if an item is in stock in the warehouse, you can have it shipped to you in a couple of days. Pricing is also really good. The bad news - if it's not in stock, or someone in the warehouse grabs the wrong thing, or it arrives broken (thanks UPS), fixing that problem is a challenge. Good luck with the call center. A good rep can grease the skids and help you handle issues. A bad one will just email you a link to the website and the phone number to the call center.
The billing office is a nightmare. Anything through the website is pretty quick, but stuff your rep brings could take weeks. Make sure when you send a check that it's very detailed. We got into a long drawn-out issue because our boosters gave the rep a check for a certain invoice, but somewhere the info got crossed and the check was applied to a district purchase, and hilarity ensued. Calling the billing office with a question is an ordeal.
Don't worry too much about the store staff. Whoever's there now won't be in a year. I send kids and parents there for any basic needs, and they do our rentals.
A good rep knows how to work the system and can solve problems before they get to you. A bad one leaves you to deal with the giant machine. I would ask around your area to see what people think of your local rep.