It's common for commercial PCBs to be made in such a way that the "fully loaded" version of a device and "budget" versions use the same board. Components are simply not populated on the budget version, and the manufacturer doesn't have to create separate boards.
In some cases, the lack of the components simply do not impart whatever functionality they provide, and nothing need be done to the board if they are missing. As a simple example, consider a board that provides additional reservoir capacitors connected in parallel, but some can be left out as conditions warrant; no connections or changes need be made if they aren't there.
However if you have a component that does actually need to be present for the device to function, then you must have some sort of alternative component if it isn't populated. This may be as simple as a resistor that is replaced with a jumper.
If the unit doesn't function correctly without the component, then that contradicts your statement about it not having an impact.
You said that one solution is to use a jumper to close the circuit, but you want to avoid using a jumper. Why? Is it something that you need to be able to toggle more easily? If so, why not use a switch? You could design the board to have placements for both the "X" component and a switch (in parallel), then populate whichever one is applicable.