Sure - If I choose, I can follow the long press with other modifiers to trigger various other macros.
a small .1 or .2 delay after release and I can tap the modifier of choice.
ie. Long Tap followed by Control or Long Tap followed by Option etc. etc.
This approach is not reasonably possible when the Long Tap is triggered after a certain 'time out'. Your timing would have to be perfect. =)
But I also do use the nice macro that @noisneil has developed, that has the long tap triggering after a certain 'time out'.
I use a Kensington Expert Mouse that has 4 buttons. I primarily us it and modifier keys as my triggers. It's quicker than modifier + key combinations since I don't have to move my hands.
To use your example of ⌥a.
I long press ⌥a then release, there is then a .15 sec delay in my macro.
If no other modifier key is pressed in that time then it executes the ⌥a + no modifier section.
But I can press ⌃ within the .15 sec and run the ⌃ section of the macro, or press ⌥ within the .15 sec and run the ⌥ section of the macro etc etc.
Do you mean are the wrong macros getting triggered? No.
I could see this being a USB issue if it was just my mouse or external keyboard, but the fact that my MacBook Pro keyboard is having this same issue seems to suggest that it's not a USB issue, though I could be wrong.
Also, I'm having no issue with basic "is pressed" triggers, whether from my mouse or external keyboard or anywhere else. They all work correctly.