If you are reading both IFC files in the same workspace, both of the coordinate systems created by reading the models will exist while the workspace is still active. You can use a CsmapReprojector to reproject both sets of data to IFC_COORDSYS_0, which will be the coordinate system created by the first reader. This will not appear in the Coordinate System Gallery, but you can type it directly into the destination coordinate system box in the transformer.

Features already in IFC_COORDSYS_0 will not be reprojected, but the features in IFC_COORDSYS_1 will be reprojected to IFC_COORDSYS_0, resulting in a common coordinate system. Be sure to set the Vertical Handling as above, to ensure a 3D reprojection.

If you prefer to get the features in IFC_COORDSYS_1 instead, you may need to add a FeatureHolder before the CsmapReprojector, since that coordinate system will not exist until the second IFC file is read. The FeatureHolder will store the features until all files are read, before passing them to the reprojector.