No, that was and is intentional...
The Bootstrap CSS framework is loaded via the BootstrapCDN, this file controls the look and feel.
Any and all CSS additions & overrides should be put in either the /includes/templates/bootstrap/css/stylesheet_colors.css or /includes/templates/bootstrap/css/stylesheet.css files or as @lankeeyankee suggested, create a new file /includes/templates/bootstrap/css/stylesheet_zcustom.css
If you choose to do a custom download of the bootstrap CSS framework, it should be called where the BootstrapCDN link is called or overrides will not be picked up.
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