Thanks to Fabio's detailed and clever reasoning (you're very gifted Fabio), I have found the issue with the Alt mode. The problem turned out to be a defective U4391 (74LS02) that can be found on diagram 8 (Horizontal Display Logic A&B Sweep Generator). When measuring pin 3 on this IC there was no change in state (stayed low) when operating the ALT button in the "Horiz display" section on the front control panel (after checking the switch first). Replacing this IC from a butchered 465B restored the Alt mode and the scope now reliably displays two traces :)
Note that your problem might be caused by a different component failure or break in the Vert Alt Sync path, but if you follow Fabio's excellent diagnostics, you will find the problem. Good luck, and another big THANKS to Fabio, I owe you a drink!