Is there a way I can customize the application names in the Application folder?
you are right changing the names may have unforeseen consequences later.  

You can make a new folder somewhere. Named Apps. Or what ever you want to name it. 

Then create alises to the applications Placing the aliases in the new folder. 
You can name the aliases what ever you like and have the new folder in the dock. 



1, Create the Aliases. Drag Applications to your new folder.

They should automatically choose to be alias files because you are dragging from the Applications folder.
The cursor should become a curved arrow while you are dragging. If not then hold down the alt+cmd keys to make the copies allies files.









2, Now rename the alias files what ever you want. This will not affect the real files.

I have just named some of them here




3, Place the Folder in the Dock. And now when you go to it the Alias file will look like the real apps. Have your names and open the real apps.





You can Also just place any of the Alias files directly on the Dock.