Also, different healing cards are more effective for different situations. Healing spells are obviously good for when you want one last burst of healing to increase your winnings, or for when you need just that extra bit of health to survive. Empathic bond is good for healing large amounts over multiple turns, for long drawn-out games where you have lots of creatures. It can be good for elemental masteries, but at the same time you have to make sure you get the timing right with it (so that you actually get to full health before you kill them, instead of killing them halfway through your attack step). Shards of gratitude are great for quick games because of their low cost. They are the best form of healing available in terms of getting elemental mastery by decking the opponent out (or killing them with a weapon, if you have a sundial out to stop your creatures from finishing the enemy off). As you can see, i have just brushed on some of the possible situations you could find yourself in. Different forms of healing have different advantages and disadvantages.
Now look at it this way: say all healing were to happen at the same time (maybe you get all your bond heals, permanent heals, and card heals before creatures start attacking, but after you press space to end your turn). Now cards like the life "heal" are pretty much useless because you could just use a few shards of gratitude to get the same effect every turn. Empathic bonds become even better for EM's. Now the healing cards would need to be balanced in some other way. Maybe your shards would heal less, maybe the heal card would heal more, maybe empathic bond will cost more...who knows? but that then creates more and more programming tasks, changing the game mechanics around (and possibly modifying AI to react to the changes more effectively) for what is currently an almost insignificant issue, if it can even be called an issue.
Yes, i can see that this makes it harder to get EM on a mono-deck, but mono-decks are meant to be specialized, and the only colours with good healing capabilities are life, light and darkness (and earth, kind of with stone skin or whatever it's called, but that doesn't affect masteries). Other mono-decks have other advantages such as immortality, better defensive capabilities, better offensive capabilities, etc. Some decks just weren't made for EM victories.