Finally got around to trying to fix this again and did so successfully. 
The fix? Copy my downloaded/custom themes from .themes, .icons, and .config/kvantum to the root folder. That’s it! It was really that easy the whole time. 
Now, dolphin and dunst, and even qt5ct are rendering fonts and other UI elements at the expected size.
Note: This is an issue I probably would not have if my themes were installed from an official repo or the AUR.