Since i start working on SharePoint on-premises 2013 & 2016 & online, usually some of our customers want to have their intranet UI to look totally different from sharepoint default UI. so they provide us with a master page + cusotm CSS. and i apply it to all the site collections.
but lately with the advance of modern experience in sharepoint online. seems modern experiences will ignore any custom master pages and custom CSS, so I am not sure how we can apply our customers' custom master pages and CSS files? in other words, if they want to have a custom master pages and custom CSS, then they need to stay working on the classic experience? and they can not combine working on the modern experience and having custom master pages and custom CSS ?