Looking at the general charts in WWS, the total amount healed that is shown is effective only, and doesn't include overhealing. When you look at your character breakdown for each heal cast, the amount it gives you for each heal is total healed, not effective. Looking at my WWS from last night:
Wow Web Stats
My effective healing was: 4,697,248. On my character breakdown sheet, my total healing by Holy Light was 7,481,125 which means the stat shown is total healing and not effective. Going off that, my total healing for Beacon of Light was 994,691 with 51% overheal. So that would actually give me 10% Beacon effectiveness (which is default in Rawr) if I only wanted to include effective heal.
The only thing with factoring in overheal, though, is that Rawr doesn't currently take this into account. It's just looking at the total possible healing output, right? So since your Holy Lights, Holy Shocks, and Flash of Lights aren't taking into account the losses from overhealing, beacon and glyph of holy light would be incorrect proportional to how the others are counted.
So would it actually be correct to set your percentages based on Beacon of Light and Glyph of Holy Light based on total amount healed, not effective?
Edit:
i also just realized another error in my calculation where I was looking at my total effective healing. i've actually got to take out judgement of light and glyph of holy light, since they don't proc beacon.