Edit 2021-08-02:
“obsidian.css” has been deprecated in Obsidian Release v0.12.12 (Insider build). The main request has been updated for current situation.
Obsolete proposal:
When opening the settings/appearance, detect whether “Obsidian.css” exists in root of the vault. If not, then do not intrude users by legacy option for “Apply custom CSS” but instead show option (checkbox/switch) to temporarilly disable all snippets at once.