The first quest line serves three purpose
1. ) It is meant to start with the player as the progress from the very start, so for players that had been playing before 0.1.7 it might not make as much sense in an older world. But more then that almost every quest is aimed at the progression through the default Minecraft achievements. The reason for this is to help unlock the inventory slots that are locked so that the player finishes the first series of quest with some fair inventory space.
2.) It intends to show players that I haven't in any way tinkered with the default nature of minecraft.
3.) The pack is almost primarily developed for myself and a group of friends, a lot of whom aren't really familiar with Minecraft so I wanted to give them a guide, because in a lot of ways Minecraft on it's own simply doesn't have a guide. HQM is more there as a guide for players wanting to understand what the mods do more then anything else.
As for Ars Magica 2, my understanding was that the Mod Was fairly unstable and no longer being developed.