I just tried it (for the first time) and I certainly *am* able to make an alias of the Masters folder, as well as any of the individual folders inside it. There was no difference in the Finder, for any of them. I'd be curious to know what's so different about your system that is preventing you from making an alias of the Masters folder. I'd still suggest that setting up aliases for the various years would work fine, even on "auto-pilot." The only catch is that you'd need to remember to make a new alias in 2016 and each year thereafter. (Of course, within a few months I am *sure* Google will update Google Photos Backup to recognize the Photos database natively... none of this "alias" trickery required, so the point will be moot.)
I'm also wondering why, inside the Masters folder inside my Photos Library package, I only see folders for 2015, 2014, and 2013. I find that odd because my Photos database has photos going back to the year 2000. Where are the folders for 2012 and earlier?
In any case, on my system Google Photos Backup is working just fine, pointing to the parent folder that my Photos Library folder is in (~/Pictures.) I'm not sure why this isn't working for everyone, but it's certainly working for me.