Open files with same extension in different directories with different applications
That is possible with Folder Action.

Means your files have to be in separate folders.

I assume you mean Folders when you say Directory.

As step one lets create a Automator flow for Folder Action.



Step 2 select the folder you want and create the work flow by dragging following in to it. You are done with this step, save it under a name you want for future references.



Step 3: In finder right click on the folder you want this to work on and select Services- Folder Action Setup..

In the pop up window select the file you just created. (yourfile.workflow)



That's it, now all files inside that folder will be opened with specified application, so you can now set that for other folders using the above procedure to set other applications to open same file type. It will do it automagicaly from now on as soon you drop a new file in the folder.