It seems there is literature on the topic showing general agreement between groundwater flow from all subbasins and the output from a baseflow filter program (see attached Allen et al. 2000). Yet I'm uncomfortable using groundwater flow from the subbasins. It would seem there's a logical inconsistency in that the subbasin approach does not account for the temporal lag from subbasin GW flow (subbasin ground water to reach, and then reach routing procedures to the catchment outlet). Is that lag not meaningful? Additionally, looks like there are other reasons for not conflating groundwater flow with baseflow. See the bit below taken from Price 2011 (also attached). Again, sorry if this is all obvious to others but I'm just getting into the subject.
"Several sources emphasize that ‘baseflow’ is
not synonymous with groundwater flow, as it
includes water transmitted from shallow unsaturated
storage in addition to significant contributions
as hyporheic flow from phreatic storage
(Anderson and Burt, 1980; Brutsaert, 2005;
Buttle, 1998; Ward and Robinson, 1990). In
addition to bedrock water storage, baseflow is
also derived from the drainage of near-surface
valley soils and riparian zones, as water concentrates
in these areas during and following precipitation
events (Brutsaert, 2005; Smakhtin,
2001)...."
Thus, I think I'll use a baseflow filter program. I'd be interested to hear alternative opinions though!