How to download file under same filename?
There is no way to override that &quot;feature&quot; permanently.  However, there are a couple of workarounds:
Hold the Option Key
Hold down the Option key when you click on the link and it will tell Safari to overwrite the file if it already exists.
I just tested it on Safari 10.10.3 and it works as expected.

Use Download Linked File As...
You can also specify interactively if you want to overwrite the file using the Download Linked File As... option.
Click on the link while holding the Control key (or right click) and you will be presented with a context
 menu.
After the &quot;Save File Location&quot; dialog box, if the file exists, you will be prompted to Replace or Cancel.


Set Safari to alway ask where to save downloads
This is done in Safari Preferences (⌘, while in Safari).  With this set as Ask for each download. if the file you are attempting to save already exists, you will be presented with a confirmation dialog as above.