You realize that there are two sides to every internet connection right? It doesn't matter if you are running your end through a VPN, they can slow / filter it from the content provider to you.
Presumably they are talking about a VPN service hosted somewhere outside of your ISP's network, so your ISP could only throttle traffic between you and your VPN service but not between the VPN service and the content provider.
The VPN's ISP or the content provider's ISP or any transit provider in the middle could throttle between the VPN service and the content provider, but there is far, far more competition among ISP's suitable for server farms and transit providers than there is among residential ISP's so they are much less likely to be able to get away unreasonable throttling.
The traffic isn't completely circumventing your last mile ISP. Just because you tunnel over that connection doesn't mean they're not serving your traffic.
Likely the outcome would be "we couldn't identify this traffic as one of our approved providers, so we used the lower of the rates we offer."
e: the second bit of that was to compare to the plan offered by a peer comment, with e.g. netflix, youtube served at higher rates and the rest at lower. So you would never see the higher rates.
