I dont quite understand what you are asking... an XDF is basically and xml file to match the bin adresses in a proper format as I understand it atleast.
You can load basically any xdf with any bin , and if you gonna open the maps its still going to show  binary stuff, but obviously they are going to be wrong data.

So you correct the maps(adresses) that you gonna be using for your tune and thats it.

Essentially what you are asking  I guess, is that is it going to affect the bin saving by having adresses wrong within the xdf, and some of them are right, and the answer to that is no, I am pretty sure.

If I am wrong someone correct me I am just trying to help with my limited experience