Enabling the HTML with currency option will allow the settings inside the Shopify Settings > General > Store currency to apply the styling if set. Since the HTML with currency often inputs its HTML code inside of the theme, often, when there are issues with pricing displaying incorrectly, unchecking this setting, will resolve them.
More information can be found from this Shopify article:
https://help.shopify.com/en/manual/using-themes/change-the-layout/help-script-find-money-formats