A lot of those knobs are actually pretty useful, especially when there are competing implementations of a standardized interface that have different strengths.

A lot of those knobs are actually pretty useful, especially when there are competing implementations of a standardized interface that have different strengths. As an example: In scientific computing this often means choosing a particular BLAS or MPI implementation when compiling, sometimes based on the data in a particular run. Not saying autoconf is awesome (I curse it on a regular basis), but the configure step itself is worth keeping around.