It's not "we need to keep compile time down to seconds, therefore configure in the source"; it's "compile time is seconds (if that), so there's not much difference between configuring in the source and configuring in a file except complexity". One part of the motivation for the best practice you cite is that compiling can be complicated and take a long time, and configuration changes should be quick. This is a solid argument against that portion of the motivation. Following practices because they are known as best practices when the motivations for those practices don't apply has another name - cargo culting.

Edited to add: Which is not to say that this best practice should be simply discarded, but to say that the appropriate response is to point to the other motivations for it and determine whether they are more important than the upsides of configuring in the source.