The first example is more likely congestion than throttling, but that's only really a difference in the manner that your ISP is being cheap (and not having enough bandwidth upstream).
Using a VPN in this case is probably causing your traffic to take a different route than everyone else's youtube traffic, thus avoiding the congestion bottleneck.
Netflix may have a local cache nearer to you, so you don't hit the congestion (and the amount of content in a Netflix cache is probably a lot less than Youtube).
Example 2 could be a packet-lossy network which causes your TCP connection to ramp back. If it's constant packet loss, your TCP connection will probably get slower and slower: TCP uses packet loss as a signal it's going too fast, but if that's not the cause of the loss, your connection will just keep getting slower.
> but that's only really a difference in the manner that your ISP is being cheap
Doesn't that depend on the peering agreements? How do you know it isn't the case that problem at the links isn't due to the video service paying for insufficient bandwidth?
Whenever you send a packet in TCP, the recipient sends back an "ACK" packet confirming receipt. If some timeout interval passes, the packet will be sent again. This means that some packet loss will not interfere with a TCP connection.
This is used for congestion control: Imagine you have a computer with a 1gbps LAN hooked up to a 100mbps network. You can send packets at 1gpbs over the LAN, but 90% of them would be dropped at the speed change point. The TCP stack will notice it is losing packets, and will throttle itself accordingly.
TCP is actually more complicated than just this, but this is one of the more important parts.
Packets can be dropped and TCP will retry (among other things; packet loss is a hueristic.) It won't just cut the session on some amount of packet loss, that would lead to constant failures.
Using a VPN in this case is probably causing your traffic to take a different route than everyone else's youtube traffic, thus avoiding the congestion bottleneck.
Netflix may have a local cache nearer to you, so you don't hit the congestion (and the amount of content in a Netflix cache is probably a lot less than Youtube).
Example 2 could be a packet-lossy network which causes your TCP connection to ramp back. If it's constant packet loss, your TCP connection will probably get slower and slower: TCP uses packet loss as a signal it's going too fast, but if that's not the cause of the loss, your connection will just keep getting slower.