I can’t comment on the shop in Berlin, but the one in Paris is a special case. It’s in a relatively central location in a 11M people metropolis, right on top of a major rail and metro hub and across the river from one of the most touristic monument in the world. And even though it’s not really in a shopping area, there are dozens of cafés within 2 minutes on foot. They don’t really have problems getting people to go there. Plus, considering how long hey’ve been in business, I assume they own the building, which shields them from the rent issue. They could still face problems (like Gibert next door that closed somewhat recently), but their situation is very different from the vast majority of shops in normal European cities (including the UK).
Yeah, I walked by the block-long line of people a couple months ago and pretty much crossed it off my mental list. Didn't need another physical book and there is no shortage of cafes in Paris. Also didn't even make a special trip there. I like to stay in the Latin Quarter and happened to be walking by.
I agree it's not exactly the random indie bookstore though as it's probably listed in every Paris guidebook.