I have a QGIS project that uses data stored in Web Mercator (epsg:3857) spatial reference system. The project itself has epsg:5514. To have a better precision I use one of datum transformations that are available for this srs. This datum transformation is set on project level. On the QGIS Destkop works everything perfectly but when I use the same project in QGIS Server, the data are several meters shifted. It seems that QGIS Server does not work with datum transformation that are specified in project file.
I have the same issue. I've found a mailing list correspondation here: https://firstname.lastname@example.org/msg35582.html. But this adresses to QGIS Server 2. We have a working solution in QGIS Server 2, but it doesn't work within QGIS Server 3. So if there is anyone who have an idea, what changed in version 3, that will be awesome!