Cannot reproduce this in Pro 2.0 / Portal 10.5.1.
The Consolidate Project tool publishes -- although this tool provides practically no use publishing it by itself as a web tool. The output is a directory which will be hardcoded, thus nothing returned to the end user. The input, an APRX is essentially a pointer. If you 'upload' the APRX from a client machine to the server, its not uploading all the components of the APRX, thus the consolidate project tool will fail.