They may secretly start throttling you/adding latency to get you to call back. I may be crazy, but after I renegotiated a higher speed for a lower price, I have been having all kinds of crazy latency/timeout issues that don't happen on a VPN.
I have custom DNS setup, that didn't seem to improve it much.
BTW traffic being faster in a VPN is pretty common for ISP throttling, for whatever reason.
But like you said, it's not useful to us as a customer of an ISP because we can't alter the routing table used by the ISP even if we identified a problematic routes/peers. You can try to complain to their customer support, and might get lucky if the customer support has technical authority to debug peering issues.