Roasted
You're right. roof_colored.shader affects all roof parts.
i've further tightened the conditions to only make roof decals visible for roof pixels at exactly 5% (+/- 0.1% errors) transparent (glass armor sprites). Hopefully, this would scrub modded roofs clean in most cases.
You might install latest glass_armor mod package to see if the fix worked in your case. (updated on 17 Nov 2020).