Yes - by setting the parameter autoPROC_PointlessExtra to the location (absolute path) of a file containing standard POINTLESS keywords. E.g. to change the value for the TOLERANCE keyword, we would
1. create a file /some/where/pointless.extra containing e.g.
TOLERANCE 5.0
2. running autoPROC with the additional setting
% process autoPROC_PointlessExtra=/some/where/pointless.extra ...
Of course, any other keyword understood by POINTLESS would work as well.