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The only “disadvantage” is that it allows you to do a lot more in your project page. This means that if you are not sure what you are doing, you might accidentally disable features, or make your page less good-looking.

A good example is, changing the appearance of your page, moving things around, but suddenly when someone views your page from a mobile device, half of the page is not shown correctly, and some elements are hidden behind others.

Another disadvantage (and possibly the reason you have to request custom CSS manually) is for consistency. Once a user views your page, they will likely expect certain things to be in certain places. If with CSS you move things around, some users might spend more time than usual looking around.

Other than that, there is no direct disadvantage, only what you may cause indirectly.