Testing a board without placing a component
There are lots of ways to avoid jumpers. You can use analog switches, digital switches, mechanical switches or other means of customizing a board such as external connections, traces which might be drilled out to open a short for the 'high end' version, solder shorts etc. 

It's very difficult to give specific advice without knowledge of what the part and limitations are. Generally a machine-mounted 0R resistor will be almost free, so that would be my first choice if it's a variant decided at manufacturing, never to be changed. Then your option is to place expensive component X or (almost free) component Y. If you need multiple shorts, a machine mounted 4-resistor 0 ohm array is very, very cheap and uses little board space. 

You can even buy big expensive-looking 'PQFP' chips that include shorts internally, which you can get house numbered so your design is harder to copy (but they're not cheap).