throttling and congestion both drop packets in a TCP stream, which signals the sender to slow down it's sending rate. congestion means that the packets are lost because they can't be pushed through a networking device (because the output port is busy and there isn't enough buffer, for example if the peering link between an ISP and a busy content provider is at maximum capacity); throttling means there is enough buffer, but the networking device is programmed with a policy to drop packets from certain streams (for example, those with an IP address originating from a content provider)
A VPN circumvents congestion or throttling not by virtue of being encrypted but by having a different source IP or traversing a different route & different network ports/links from other packets going to the high bandwidth use content provider(s)