I visited the Dalton hideout a couple of summers ago. Pretty cool.
What you call theme dependent is WordPress’s strength. In fact theme and plugin development are closely related so learning to build themes is like learning how to use the plugin API to boot. So I hope you don’t think of that as a bad thing.
If you haven’t already done so I would check out the “stepping into templates” page in the codex:
https://codex.www.ads-software.com/Stepping_Into_Templates
That will help you find your way around any WordPress theme. Once you understand the structure of a theme they are all the same. In many cases you can make hundreds of site designs while barely changing the markup of a given theme at all and just editing the css (style.css which IS your theme really) and maybe a few functions (functions.php which is the DOer of your theme) assuming you started with a robust theme template markup base.
I hope that helps. I would be more specific but when I looked at your site it looked like you were in the middle of breaking everything to learn how it worked. I’ll look again if you post again after you’ve gotten a little further along.
Find your day well.