I’m basing my statements on an early proposed patch to address this matter. @epourmal (@epourmal1 ?) stated the following then:
On Friday, March 27, [2015], we reviewed the patch and concluded that we cannot accept it as it is. Applications that rely on the current behavior will be broken.
If this could be changed now that would be great. Having the external files be relative to the HDF5 file as the default makes a lot of sense to me especially with heterogeneous networked file systems.