I ran into the same problem and implemented a workaround as you suggested. However, there is an important point here that should not be missed: we should be able to trigger the direct click functionality via programmatic keypresses, not just physical keypresses. This has nothing to do with Eyex for Windows, since the direct click concept (activation key) is part of the API. Otherwise, software designed with your API will not be accessible, e.g. by Dragon NaturallySpeaking users.
Specifically, you can reproduce this by trying to send the direct click programmatically using the standard SendInput function:
I can remap the direct click, but that doesn’t fix it. I’m a heavy Dragon NaturallySpeaking user and this is the first time I’ve ever seen this happen, so it would be a big surprise for many users.