FYI for anyone else facing this problem: After migrating to A6 6.60, the dll is not loaded before the engine compiles the C-Script, so the 3dgs icon remains for as long as the splash screen is present and the code is compiling. Presumably A7 switches the icons before the code compile. I just haven't verified this. When A7 is stable enough to come out of Beta, I'll give it a try.
In the meantime, if anyone else has any ideas for how to control the engine's icon in the taskbar from the moment the engine starts up, I'm sure there are many others out there who would be interested. It's rather embarrassing to put a product on the market and the first thing the customer sees is another company's generic icon while the splash screen loads the game. (Honestly, icon control should have been a no-brainer feature for Conitec's product marketing department years ago.)