Originally Posted by
Yayanotherlogin
I'm far from an expert, mostly just going off my own experience as a Pay-In beta tester (aka, anyone who buys the games before the 3rd or 4th patch) with Fallout 3, New Vegas, Oblivion, Skyrim, etc. That said, in my experience, going step by step as in example 2 usually won't break too much, but sometime does not trigger NPC dialogue paths, reactions, etc. For example, I used similar commands to complete the random SPAM Thieves Guild missions, but had much better luck initiating the quest by speaking to Vex or Devlin (SP?), using the console to complete the intermediate stages, and then speaking to them again to complete that quest.
Sadly, as far as I know, you really would need an very good understanding of a particular quest, its affected NPC, scripts, story branches, rewards, etc, to truly close it safely from scratch with the console. The more complex the quest, the truer that likely is. At least at a casual level of understanding, these commands are useful tools for fixing a bug, but not an easy path to skipping tedious quests with one nice big batch file.
Good luck with your research, and by all means PM me if you ever nail down what you're shooting for, here. :-)