When editing sampled data files and viewing them in the time or frequency domain then Audacity can be very powerful.
While Audacity does support some scripting functionality (https://manual.audacityteam.org/man/scripting.html), I often find that Sox (http://sox.sourceforge.net/) applications for pre-conditioning the audio files, extracting a section of audio or shortening a .wav file then I will typically use sox from a script.
On the other hand, if I want to do something more complex such as visually aligning the data in two files then Audacity is much more convenient for a small number of files.
For aligning a larger group of files I would typically do this using a correlator but that is a subject for a future blog post.
Evaluate the Numerix-DSP Libraries : http://www.numerix-dsp.com/eval/.