Hi,
Very good question actually:
One scene to do it all is good for small projects or projects very well organized in terms of elements loading, per context, per needs, etc etc, so to scale properly. A one scene project must be carefully crafted and design prior starting development. A multi scene projects is easier maybe to understand what's going on and somehow relate the user experience per scene ( one scene for the lobby, one scene for a room, one scene for a particular game, etc etc). Multiple scene will be easier to manage for large scale project when you have little experience, and can't really draft a framework to handle it all. Multiple scenes will have a smaller hierarchy content and therefore easier to grasp as you work on it.
Multiple scenes do not have to be painful to work with as you seem to say: I have designed my first big projects in Unity using one scene per page, and I could launch a single page on its own, because I designed my high level managers to exists in each Unity scene BUT could only exists once during the playback, so when I was working on a particular page, that page had all the managers and setup it needed to run as if part of the app ( and I could even configure them for particular contexts to replicate different states within the application, and when I was really starting the app, as I loaded then pages, the managers inside these pages would simply be destroyed, or disabled, or simply doing nothing, self aware they where part of the running application, not part of the development routine.
So in all cases, large scale projects WILL require some kind of framework, regardless of your approach and a clearly defined way for development and runtime. That is true, even for a one scene project ( as it doesn't seem that difficult to manage at first glance), because then you'll find you can't load it all in one go, else the initial loading time it inacceptable in 99% of the cases, so in the end it's really a matter of taste.
If you are beginning with all this, you will find pros and cons on both approach if you don't have any experience so far. I tend to design using multiple scenes, as I explained, but on the photon case, our goal was to replicate exactly the photon demo sample, to show what playmaker could do.
bye,
Jean