I came across a compilation issue with gdal after switching to this new clang. For some reason, open/close/read/write cannot be found -- as if <io.h> was not read. Then got fed up with tracing the includes where they end up and simply added those declarations to the failing component in gdal, and it worked.
I am afraid I will need more info about this as well - I have just tried to compile my 'major project' which is using UppHub gdal and it seems to work out of box. Do you even mean UppHub gdal?