Can all of the features of GraphPad be specified through a scripting language?

Prism does have a scripting language.

Prism files or templates link data (and info tables) to analyses and graphs. Change a data (or info) value, and Prism updates all linked analyses and graphs automatically. Prism scripts can open Prism files, import data, change info constants, and export (or print) selected results and graphs.

Prism scripts are usually quite short (and the scripting language is easy to learn) because the script does not initiate analyses, change analysis choices, create graphs or modify graphing choices. All analysis and graphing choices are created using Prism the usual way and saved in the Prism file (or template). The script is short and simple because it only has to specify which file to open, where to import data and what to export.

Prism scripts can be launched from within Prism, or from another Windows program via OLE automation or from a Mac program via Applescript.

You can learn about scripting by reading the last chapter of the Prism User's Guide, which is shipped with Prism or can be downloaded as a PDF file.