The shallower flange distance provides lens designers with more leeway, so that the extra space and weight available can be utilized to make faster lenses, or more complex and corrective lenses compared to an SLR lens of the same focal length and speed. My Contax rangefinders, for example, had very compact lenses of incredible quality (e.g. 45mm f2) but nothing especially exotic. Leica on the other hand brought out various Noctilux models (e.g. 50mm f1) that was superior optically to its equivalent Canon and half the weight. And probably five times the price.
The advantage was most likely down to little compromise on design and cost, but it was there. Current mirrorless lenses appear to going the Leica way of both incredible optical performance and cost, no longer constrained by the mount.
I mean, you've as much as said this, I just thought to add some anecdata. A key driver of these improvements have of course been the ever-increasing resolving power of the sensors needing ever-better lenses. The Zeiss 45mm is my favourite lens ever, but I would not pretend it has the resolving power of a lens made in the last four years. There is of course, more to a lens than resolution, as the Zeiss 50mm C-Sonnar which I cannot part with proves...
I am very impressed with modern mirrorless cameras and lenses, but it is unlikely I will personally be able to dive in, on the grounds of cost.