Apart from the technical arguments for retracting or leaving the gear and flaps in position after a GPWS or windshear warning, there are practical and human factor issues.
With gear and full flap, a retraction procedure may require two sequenced operations and a revised speed schedule, but with intermediate flap and/or gear up, there are likely to be different procedures; complexity aids confusion.
The human issues are that even experienced pilots will encounter some surprise or shock after a warning, this affects the ability to recall drills or it may delay action; some manufacturers considered this, and their consensus was to focus on the important issue of pulling up quickly using the correct technique (FSF ALAR/CFIT Task Force). A quick review of CFIT accidents identifies that a large proportion occurred just below a ridge or hill top; 60-100 ft. This indicates that the most important time during an encounter is the first few seconds; here excess speed can be converted to altitude without concern of stalling or any longer term effect of drag.