I see. The only way I can see this might be possible is if you write a custom tool. Custom tools are a feature that allows you to add items to the Tools menu that run Java code. This is a bit confusing because you can also add custom tools menu via boards.txt but that is more limiting.
I haven't found much documentation on this. If you look in the tools subfolder of the Arduino IDE installation folder you will find a file, howto.txt and also two tools. The first one, Mangler, is just there as a demonstration of how to write a tool. It's not compiled so that's why you don't see a Mangler entry in the Arduino IDE Tools menu. The other is the "WiFi101 Firmware Updater" you will see in the Tools menu. This was added in Arduino IDE 1.6.10. 3rd party tools can be installed to the tools subfolder of the sketchbook folder. This is a bit confusing because hardware packages also use the term "tools" and a folder named tools for their toolchain but these are two separate things and the folders are located in different places. This tools system is also used in the Processing IDE, which actually has a selection of official and 3rd party tools available. You may find more documentation for tools as they relate to Processing:
The only 3rd party tool for the Arduino IDE I know of is the EspExceptionDecoder:
I don't know whether it's possible to use a tool to set the path that will be used for the Tools > Burn Bootloader command.
If it is possible, the issue arises of how to package the tool with your hardware package. I don't know whether it's possible to include this sort of tools with a Boards Manager installation and I haven't seen it documented anywhere. The only thing I can think of is to treat it just like the other sort of tool (toolchain) but I'm doubtful that the Arduino IDE will recognize Java files in that location. It's also a bit awkward to bundle with a manual hardware package installation because the hardware package files are installed to the hardware subfolder of the sketchbook while the tools are installed to the tools folder of the sketchbook. I suppose you could have that full folder structure and have people copy the whole thing over their sketchbook.
Sorry I'm not able to be more helpful in this. It may be a dead end but I do think it's the only hope to achieve your goal. Maybe someone else with experience in writing tools will comment.