Yes, Best-Practice can mean something different for everyone.
I have found, in the past 8 years of using Seamly, that it is best to start by drafting a basic pattern that includes Variables in the Variables Table for ease and other things that one may want to change from one design to another. I’ve also found that drafting the basic pattern using a Standard Multisize measuring chart allows me to check that the curves remain curves when I change sizes while drafting my basic pattern. This way, when I load an individual’s size chart into the pattern, the curves will still be smart (within reason - it depends on how close a person’s measurements are to the standards).
As for the ‘Over-Engineering’… relax and enjoy the trip. It’s a learning curve and I feel lost if I don’t design something almost every day. It’s a challenge that you either take up or drop - your choice.
You can pick up almost any patternmaking book, or find something on the internet, and the 1st thing they teach you is how to draft a bodice and the 2nd thing is how to draft a sleeve. Most even give you standard measurements to create your multisize measurement chart from.
Follow those directions in a Seamly fashion and you’ll have your scaffolding resizing when you change the size and then your pattern doing the same without the box-in-a-box-in-a-box.
As far as curves are concerned… I posted a bit in this post to get you started, but there are many other posts on the subject that can help you if you do a search. Check them all out and you’ll eventually devise your own personal way that works for you.
Once you have a basic pattern drafted that you’re happy with, save it as your master. This will be the foundation of every other pattern that you create.
When you want to make a new pattern, open this master and save it to the new design’s name, edit the ease (if you wish), and do your design over this master. You can rotate the darts, add design ease, move things, add design lines, draw in a new neckline, whatever you want, just don’t edit the formulas of the original design.
With all of that said, you can also find basic patterns for shorts or trousers and the same things apply.
I guess I’ve told you all of this before, but now it’s in writing. 
And it may help any number of users.