I came back to my project after a long time and I noticed flickering of the pixel-thin edges of some of the tiles in my tilemap when moving around the layout which never happened before, so I was expecting some Construct update to start causing it. I read a lot about it and tried changing all the downscaling options and pixel rounding and experimenting with tile sizes etc. and nothing helped. Only when I tried changing the "Z axis scale" from Normalized to Regular, it solved the problem.
My game is top-down 2D so I have no idea why this setting was causing it but I just thought I will leave it here for anyone who might experience the same problem with pixels flickering.
I'm still curious why this settings was causing it though, so if anyone understands it and have some time to educate me, It would be great to understand.