It's not really a bug, it always worked like this, but since nobody is courageous enough to maintain some real documentation, it was lost.
Anyway custom inputs inherit inputs from defaults of course and what is saved in custom inputs is only what you changed !
That's why by editing some default inputs you can affect games using the custom ones.
I must say it's a little strange to save only what was changed, but it always worked like this since... err no not since the begining, actually it worked like this since the switch to sdl apparently, so since 0.50, it was an error on my part when rewriting the inputs code...
So for example if you set custom button 1 to v in sailormn, then set default button 1 in another game to something else, sailormn will keep its v since it was saved in custom, but if you edit any other default input, it will inherit it.
And you don't need to setup a new installation folder all the time, I always make sure there is no config file in the archive so it doesn't overwrite them, I can make a mistake of course, but it's extremely rare since I don't run the windows binaries in these folders usually.
Ok, I'll remove the test, it's easy to save all the inputs when using custom inputs. But I won't make a new binary just for that, you'll have to wait until something more serious is found !