Hi SPD,
custom.css file order is fully OK, why becuase that file is from template and it's loaded as the last css file from template. And this is natural order.
If you want to load your custom CSS below all the components styles - it request extra but easy step.
- Rename custom.css file into override.css
- Inside Template Options > Custom Code > Before end of < head >
add below line
<link href="/templates/shaper_helixultimate/css/override.css" rel="stylesheet" />
Then that file will be loaded after all styles from template, and components etc.
That's all. Yes, you can still edit that file from Joomla Template Editor.