Morkus from Orkus
If the deliberate design creates inconsistent(not valid exceptions) rules, that's a design flaw. If you have a rule that says people can't fly, then you create a magical fly spell that's an exception, that's one thing. There's no such in game explanation for being able to write this spell without magical ink, but requiring that spell over there to be written in magical ink. The Wizard write up says nothing about magical ink oozing from the Wizard's pores as he has a flash of insight, allowing him the ink to scribe his two spells.Why?
What I'm saying is that the book purposefully ignores ink costs for these 2 spells because the designers didn't want to tax the player for their character's evolution. It's a choice favoring conviniency and ease of play over simulationism. Maybe it's not for your group, or the OP's group, that's fine, but it's not a bug, it's a feature.
Having an issue with inconsistencies is also not simulationist. It's closer to gamist than anything else. Any game should have rules that are consistent, regardless of any intent(or not) to simulate something. If the Chess rules allowed the black player to move his knight twice every 4th time he moves his knight, that would be an equally inconsistent rule.