We have disabled the 'shopping by' function in our MGS Theme configuration, however we are now having issues with text swatches in the layered navigation. Once a swatch has been selected, it then cannot be unselected. This is only an issue with swatches, as checkboxes can be selected and de-selected with no issues

Answer: It's how theme works. By default, you can't click to text swatch to select and then click again to unselect (you can change to Luma theme to check, in Luma theme, we still can't do that). Therefore we make 'shopping by' function so that you can remove any option after filter.
And if you disable this function, we have no way to make it work.
The way text swatch and checkbox work is different. Therefore we can't compare them