Sorry, but I still do not know how / why you are using a screen layer mode for colouring. I know the how, it is the why bit 
If the background shows through it is because the 'black' still contains a proportion of white. The black becomes semi-transparent on color-to-alpha or similar.
Some possible methods shown here: https://youtu.be/NgKV055ADGc duration 4 minutes
I am not saying use this method, Gimp is very flexible, there are always several methods to do anything. You might be able to 'cherry-pick' parts of it. Hope it helps.
Finally, somewhere you will have used a GEGL operation. 75% of Gimp is now using GEGL in place of the old gimp plugins.
If the background shows through it is because the 'black' still contains a proportion of white. The black becomes semi-transparent on color-to-alpha or similar.
Some possible methods shown here: https://youtu.be/NgKV055ADGc duration 4 minutes
I am not saying use this method, Gimp is very flexible, there are always several methods to do anything. You might be able to 'cherry-pick' parts of it. Hope it helps.
Finally, somewhere you will have used a GEGL operation. 75% of Gimp is now using GEGL in place of the old gimp plugins.