The first and last of your three points are as good a way of doing this as any.
If you draw a bridge on the solder paste layer, then there will be paste placed there. You would need to make sure that the gap between the jumper pads is small enough, the pads themselves are not too large, and there is enough solder paste. You can test this out with a test board, or as your PCBA if they have any tested spec. By using the solder paste layer, the bridges will naturally form the desired bridge during reflow.
Alternatively, adding an additional information file with your assembly job is quite common. You can for example provide a too-scale drawing (even gerber file) of the location of all solder jumpers giving infomation as to which should be bridged and which shouldn't. A summary list can also be added to the BOM.
In fact doing both is a great option because it allows for the bridges to be primarily acheived during reflow and then verified during inspection. As part of the board inspection you simply state that the solder bridges should be in place as indicated in your diagram. Any that aren't can then be corrected by the PCBA house manually as a rework step.