It's not common but hardly impossible for magnesium lowers to bend or deform, I've seen it happen several times. It can often be the result of over-flexing the fork from a crash or heavy duty riding (more common with quick release drop outs, or downhill forks) and simply not springing back. It can easily be spotted by the drop outs not lining up, or stanchions not lining up when reassembling the fork. Continueing to ride a bent set of lowers will cause the bushings to wear into your stancions inside the fork, causing irreversable seal and slop issues. I'd recommend having the problem taken care of sooner rather than later. Your fork probably hasnt ridden well for a while, hence your inclination for a rebuild. The unfortunately nature of suspension is that a decrease in performance takes place over a long period of time, and is often unnoticable if you ride regularly. That's the biggest reason I stress routine suspension service for avid riders as a preventative measure. Your problem will likely be solved with a new set of lowers, it's extremely uncommon for uppers to twist or bend.
I work at another shop in the area and handle the suspension service there. From a mechanics standpoint, suspension is a bit tricky to deal with if you work in a busy shop that books by appointment only. Assume a customer makes an appointment to have their suspension serviced, but there are issues discovered only when inside the repair, much like yours. The result is the "phonecall," an even longer wait for parts (since they're small, specific, and impossible to stock all of), and an increase in the bill. Often times its an honest and unavoidable situation that can reflect badly on the shop and leave the customer without a ride. That sucks you had a bad interaction, but I'm sure it was just an off-experience. I know plenty of people who use that shop and love it. Best of luck at your next pitstop!