I am not a fan of the multi column and tab bar design.

I think a single column where sections and subsections expand and collapse would be better.
Similar to something like Sonarr:

I think that the column should always be in the current collapsed state, and it should "slide out", similar to how the forum UI slides out when you mouse over to the left, when you mouse over it. Users should be able to pin it out if they wish. I want to keep as much screenspace available for the tables.
In regard to the table, I think it needs to be denser. It seems like there's padding/wasted space between columns. Perhaps auto-adjust the columns to be as wide as the column text by default, with the exception of the first 3 columns, where they should be just wide enough for the checkboxes and icons.

Finally, the dark theme. I'm not sure what the issue is, but it just doesn't look right to me. The light theme looks great.