What is the difference between `open (-a) ` and double click in finder/spotlight?
Well, one difference is that via Command Line, you can pass the file to be opened as an argument, but I guess this is not the difference you are after.

The behaviour you speak of appears to be a bug which can be observed when running Yosemite. The issue is still open: https://github.com/leksah/leksah/issues/37