You know, I had problems just like the ones you're talking about. Except with me it was t.co URLs all the time. It didn't matter if I stripped off the extra parameters or not. It's as though Safari uses a content cache infrastructure that is shared among all the safari processes and webkit plugins running in, e.g., Mail or quick look processes, that got bogged down on a particular host, for some reason, refusing to do more connections to that host until after some timeout.
Which explains why the other browsers had no trouble: they have their own content caches.
And then that problem went away after one release. But I saw that it went away for me but was still an issue for other people, and that and the fact that Apple was trying to blame it on ISPs sometimes, plus the fact that deleting some networking config files seemed to do the trick - well all that led me to assume it was the same problem I have seen with wifi.
This level of flakiness is astonishing, really. Stuff like this should solidify over time but I think Apple keeps on innovating and with innovation comes breakage. The appalling thing is how long we sometimes have to wait for a fix and/or even just an acknowledgement. Still, as a programmer myself, I know how bizarre and complex these things can be, and when I file bugs at bugreport.apple.com, I almost always get some serious interaction with Apple to try to resolve it.
Let's hope 10.12 is everything we ever dreamed of in terms of stability. El Capitan was, in my opinion, the best release since Snow Leopard, despite this particular pair of problems that have been around for so long.
