YouTube updated its iOS app over the weekend with native support for the layout and resolutions of the latest 11-inch and 12.9-inch iPad Pro displays, but as noted on Twitter and Reddit, the home indicator now overlaps the bottom menu bar.
Two steps forward, one step backward for now, but hopefully Google addresses this issue in a subsequent update to the app. On the iPhone X and newer, the menu bar is positioned slightly higher as to not overlap with the home indicator.
Spotify also recently updated its iOS and watchOS apps with native support for the 2018 iPad Pro, iPhone XS Max, and Apple Watch Series 4.
Update: YouTube has fixed the menu bar issue in a February 2 update.