Cut off the head
There is a fundamental split in front-end-land over "web applications" right now. One side leans heavily on the "application" half of the term. The other side laments the loss of what "web" used to mean.
I'm as frustrated as anyone at how some frameworks treat URLs. It does make development tougher. But letting links be links means they have to go somewhere. These applications do not have the concept of different locations. You don't "navigate" among "pages."
I also believe strongly in progressive enhancement. You want your content or functionality to be available.
But there's a bar, and everyone decides where it is. Some folks are making content for the web. Others — despite what Mr. Penman says about browser splintering — are delivering relatively universal software.
The Patreon example is a good one. Patreon should want the greatest level of access. Denying access means creators will miss out on money. For A List Apart, yes, I should be able to suck the data (content) into Pocket. Denying that means denying me the content of the site. They can't deny the content because that's what they're offering.
At some point you make a decision. Are we leaving money, value, or the good of humanity on the table by cutting off certain types of web clients to our offering? Or are we maximizing the experience for the people we hope to help?