comma before subordinating conjunction "where"

When you include the comma, the meaning of your sentence changes:

I entered the room where the hostages were.

I entered the specific room which I knew would contain the hostages.

I entered the room, where the hostages were.

I entered a room, and I discovered the hostages in there.

To take one of your sentences:

The primal algorithms broadly correspond to implicit congestion control mechanisms where noisy feedback from the network is averaged at some sources using increase/decrease rules, which are commonly found in ...

If we add a comma before where, then we imply that in all congestion control mechanisms noisy feedback is averaged. Actually, we could leave out the whole where clause without losing relevant information (anyone knowing enough about the subject already knows that about congestion control mechanisms).

Without the comma, the extra information makes it clear that this does not hold for all congestion control mechanisms, but it does for the ones we are talking about. We cannot remove the where clause without changing the meaning of our sentence.