Because you can reuse the gems on another character. It isn't so much a problem w/ quest gems. Which I made the distinction for if you read carefully.
For example, ranking up Elemental Hit, Chain or Elemental Weakness w/o dupes or currency to buy one outright puts those gems out of reach of other characters. Not to mention the scaling of all gems in output and mana costs are not equal. This is true of quality on gems as well.
It's pretty common to see in trade people asking how to de-level a gem, or offering to trade a high level gem for the same gem at lower level or simply players expressing frustration that they have to level new gems all over again. The latter of which was daunting enough that several players from our guild quit soon after realizing this fact. Including another MMO-C mod [hehe].
These are newbie mistakes where the assumption is, "Oh hey I leveled. Time to increase the gem too!" Though in practice that is not always beneficial to the character or your overall cache.
Ranking up Spark or Burning Arrow will hardly matter. Though think for a bit before jacking up Lightning Arrow or Spell Totem. As access or mana efficiency is sometimes more valuable than an extra 1% on the gem 5 levels later.