Okay! After some testing again. I am able to confirm that it's not an issue where the transparency is working or not. It is that the layers for the blend mode and the layers visibility and transparency is not updated on change.
Issue:
Changes made to layers are saved correctly but only appear on the canvas after reopening the file, instead of updating immediately.
Steps to repro on a Rasberry Pi 500:
1. Launch Application.
2. Make two different layers,one with a square,second a circle.
3. Remove visibility on the second layer.
4.Notice the circle does is still there.
5. Save, close the Application, relaunch the Application and open the file.
6. Notice the circle disappeared, the canva was updated.