How does Visa settle funds between acquirers and issuers at day-end—what rails/mechanisms are used (ACH, switches, etc.)?

In various countries that VISA operates, it has an designated bank(s) that are VISA settlement banks. The accounts maintained within these banks are used for settlement purpose. So depending on the geography and territory, this could be as simple as an interbank funds transfer using whatever the local preferred method is.

All foreign settlements is done by doing a net-off using SWIFT between VISA accounts.