The thick plottens...
I've been having some email discussions with Peter Thierolf, the original coder of Apidya (I'm not worthy! I'm not worthy!). Firstly, he is very honoured that people are still interested in his game after all this time! He's also been very helpful in finding and going through the source code to help with my debugging efforts, so snaps and/or props to him for that.
It turns out that the bug is more subtle than it seemed originally. The two values that I thought had been swapped are, in fact, correct. That much is obvious when you see the original commented source code, but not so clear from the disassembly and hex dumps I'd been working with up until now.
In swapping the two values around, what I've done is plugged the subgame activation code into the player bullets vs. scenery collision detection instead of the player vs. scenery collision detection, as it should be. The result is that the Speed Of Light subgame works if you fire at the right place on the level instead of flying into it.
Why the player vs. scenery code doesn't work as shipped is still a mystery, but I (with Peter's help) will continue to look into it to get a proper fix for the subgame.