Nine years later, as far as I know, it's still not possible to prevent connector arrowheads from overlapping with their connector shapes - https://graphicdesign.stackexchange.com/questions/50844/inkscape-how-to-position-arrowhead-exactly-at-the-end-of-path

It would be great to include on connectors a textbox for a float, that decreases the line length on both ends for the value entered. That way you could select all your connectors, change the value to -5, and the connectors would stylishyl end slightly outside the boxes they connect.

https://inkscape.org/forums/beyond/how-to-report-bugs-or-request-new-features/