I'm working in Sharepoint Server 2016 On Premises site. I edit the site html, css and js in Sharepoint Designer 2013. When I add custom CSS style properties like transform, webkit transform, ms transform etc., I get a hover pop saying this property is marked as invalid and not supported in current schema. I have checked the schema version and it is CSS 2.1 and HTML4. Is this the reason for not accepting the advanced properties. If it is, how can I add CSS3 and HTML5 to this site? Many Thanks in Advance!
Yes, this is because your customization uses a CSS version that does not support transform (should be used in CSS3).
Per my test, I add following code in SharePoint server 2016 page with Script Editor web part, it works well.
Since HTML 5 and CSS3 is valid in the page, it will also be valid in SharePoint Designer, if this is a warning, please ignore it.