Fundamentally, it’s important to realize that this system is meant as a starting point, not the last word. Anytime you have multiple modifiers to a single DC, the potential for accidental consequences or intentional abuse is there.
To keep incantations under control in your campaign, avoid creating incantations with Knowledge (arcane lore) DCs lower than 30. Conversely, don’t allow any feat, class feature, or magic item that provides a large bonus to Knowledge (arcane lore) checks. Bonuses of +2 or even +4 are fine, but larger bonuses might unbalance your game.
GMs should emphasize how much faster, easier, and safer spells are than incantations. Every incantation you create should have at least one component that’s difficult for the caster to deal with, such as an experience point cost, expensive material component, or significant backlash. Because incantations don’t require spell slots—or even spellcasting ability—you need to make sure that characters can’t simply cast incantations repeatedly, stopping only to sleep.