You can edit configuration for the widget via the code. Here is documentation on the widgets used in Magento. You can view the widget for refinementList and the sortBy options for this. To sort facet values alphabetically you should set the sortBy value to “name:asc”. Per the documentation, to add or change the preconfigured widget, you can use the beforeWidgetInitialization event.
The setting for sortFacetValuesBy in the Algolia Dashboard won't be reflected on your Magento frontend as this setting is overridden at query time by the default Algolia Magento frontend implementation. This sorts the facets by "count" as seen in the following code: