Alignment (here not intended) and too big sizes of icons and text could be a consequence of screen_dpi_overwrite wrong setting. So it’s important to check if that or something else.
To see the correct alignment of these icons and sizes, you could also see the grey theme I made (I post a screen capture of modules icons rendering, same on dark and grey theme) from the dark theme by Aurelien here : Grey css themes for new UI on darktable 2.7 (dev), on with and the other without modules icons
darktablerc file is on this folder you mention : /Users/seb/.config/darktable/
Be sure to have -1.0 on the line I previously mentioned and of course, edit this file with darktable closed as this file store your preferences and state of last state of darktable.
For css, all default css are where darktable is installed on share/darktable/themes. If you want to customize some things, you indeed have to create a custom css on your .config/darktable folder.
On this folder, first create a “themes” folder.
2nd : create a file (for example Seb.css) and then add an @import line on the beginning of your file that point on the default css (full path of one of the default css).
Then you just add options you want to change (no need to copy all things as the @import section import by default all css and after you just write those you want to customize.