We have used a custom theme with font scheme file(.spfont) in our SharePoint 2013 farm.
The font sheme file contains web relative paths for woffsrc,eotsrc,ttfsrc,svgsrc,largeimgsrc,smallimgsrc (Example: /Style%20Library/Branding/Fonts/OurFont.eot) and this is working as expected in SharePoint 2013 when applying the theme manually or with our remote CSOM site provisioning.
We are now in the process of migrating to SharePoint 2016 and it seems that the relative paths does not work anymore. The path above will be translated to <WebAppHost>/Style%20Library/... .
Due to security reasons we cannot keep the fonts in the root site, so we are forced to use the full urls for each web in each .spfont that is being deployed.