Thanks so much @hareth !
The interesting thing is that I couldn’t replicate it using your logo SVG, but upon further investigation, I found the culprit.
It’s this !important statement reverting the @layer rules:
It was added 3 years ago, and have been overlooked when introducing @layer.
I created a task accordingly.
However, using “clean” SVGs without any inline styles, IDs, or classes remains the best approach. Even without the !important statement, you would encounter the same problems again and again sooner or later.