Palin,
The answer to this won't make you happy I'm afraid.
The good news - I figured I'd get this in first - is that overall, the settings situation does not significantly harm the productivity of EA. Yes, improvements are possible (and desired!), but you can work with EA in the meantime. But for now...
The situation is exactly as you describe, with some settings global, and some personal. Also, some apply across the current project, while others are 'sticky' and will be used in other projects until changed once again.
This probably grew up as EA went through earlier versions, and now is part of the legacy that is carried around with each new version. Several of my compatriots think of this as part of the product's UI, or "Unique Interface." [I suspect kudos go to Paolo for that one, but I stand to be corrected.]
Sadly, you just have to learn which is which.
[And, you'll have to relearn all of this when you work through automation. Many of the settings are not 'remembered' when you create new things (classifiers, diagrams and so forth) through the API; you have to explicitly set options where you've become used to having them default 'your' way.]
David