Tools for interconnect configuration

My intention was to alter an FPGA's final circuit after the Place-and-Route stage to simulate faults that may happen in a radiation environment.

To do this, I needed to know how the FPGA is physically routed, down to the coordinates of each switchbox.

I wasn't able to find any supporting documentation, readable file, or tool feature that would allow me to view the final true connections (non-abstracted) and edit them from any Altera source.

Have you explored QUIP?

It's a document package with some library files and testbench designs

The Constrained Routing File package you speak of did not go far enough in detail for me to understand how the logic elements were routed through the FPGA.

Chip Planner used abstract arrows to show the routing information,

and U of T's VPR tool did not allow me to make changes to the FPGA, and relied on hand-built FPGA models for routing. This was insufficient to my needs.

Xilinx has everything I needed (readable file format, tools, supporting documentation)