It appears Blockly has some built-in customization for block shapes. This is used when initializing the Blockly workspace in code.js:1094 - 

Blockly.Themes.Barnabas = Blockly.Theme.defineTheme('barnabas', {
  'base': Blockly.Themes.Classic,
  'componentStyles': componentStyles,
  'blockStyles': blockStyles,
  'categoryStyles': categoryStyles,
  'fontStyle': fontStyle,
  'startHats': true
});

Hats are the arc shape on top of event blocks. There are only two event blocks in Barnabas Blocks - the setup/loop block and the subroutine declaration block. If startHats is set falsey, then these arcs will not be drawn:

Therefore there is at least one method to reshape blocks through the regular Blockly API. My endless searching through projects was therefore unfortunately not very useful.

Hopefully I can find more ways, but in the meantime I'll be reversing the gulp toolchain responsible for the compressed source files (mainly the Blockly ones) so that editing is actually practical.