Yeah, smaller things like that are harder to quantify, and each one changes in importance depending upon your raid size, healer role, and healer composition. The only real way to gauge it is to take a step back and look at all of the differences and make an intelligent decision. Logs help, but they will change to a small degree every single fight and don't tell you things such as "Your Light of Dawn hit targets with 2 seconds left on Illuminated Mastery six times in the fight, thus extending the duration! Those same targets were also damaged 9 seconds later, consuming the full Mastery."
For Light of Dawn...
Pro: Light of Dawn has lower Overheal, since it's six smaller heals on different targets. It is chosen during periods of raid damage when everyone needs healing. The smart heal function ensures less waste.
Pro: Light of Dawn will refresh any Mastery you currently have on those six targets by 15 seconds (beacon transfer does not refresh beacon unless your beacon is one of the six targets). This is stronger on 10-man than 25-man.
Con: If you have not healed those same targets within the last 15 seconds, however, there is no refresh benefit, and the randomness of chosen targets does not guarantee success. As well, Light of Dawn is often used *solely* when there is raid damage. Once raid damage ends, if any of those targets do not take further damage within 15 seconds, Mastery is wasted. For many bosses, raid-wide damage happens in chunks, meaning that this is often occurs frequently.
Pro: Light of Dawn focus allows Sacred Shield selection, which is a very powerful tank healer. Pre-emptive healing is beautiful.
Con: Sacred Shield is two (or more) global cooldowns each minute, which is a loss of an efficient Holy Light at worst and no difference at best if there are enough brief rest periods during the fight.
Regarding Eternal Flame...
Con: Eternal Flame has a greater chance for overheal on the healing portion, as it is a single target heal. This could especially be the case when a crit occurs.
Pro: Eternal flame places a 30 second HoT on the target, giving you an effective 45 seconds before Mastery is wasted. This HoT will renew your Mastery on the target every tick for the full duration, both Mastery that is already on the target, as well as any additional heals you hit that target with during its duration. Eternal Flame complements low-to-moderate degrees of raid healing, and is stronger in 10-man.
Con: Eternal Flame has a greater chance for wasteful heal sniping; as an instant heal, you would often choose the lowest health person in the raid. If it tops them off (or close to it) at the same time as another healer chooses to heal them as well, the other healer has wasted heals which is sad. :( This is most evident when healing with a Druid class that uses less immediately obvious healing (that is also instant) than with a Smart Healer, such as Disc, Shaman Chain-Healer, or Monk, in which case their spells will automatically shift to a different ally.
Pro: Eternal Flame is easier to use as a Holy Power dump than Light of Dawn (unglyphed), especially comparing 10-man to 25-man, since while you can often find one person that needs healing, finding six can be an issue. And as you can see from the above numbers, it is less efficient healing to go halfsies on LoD/SS/EF/WoG than it is to go fully one way or another.
Pro: Eternal Flame is simply stronger HPS than the Light of Dawn/Sacred Shield combination.