I would agree this patch is not laid out in a particularly comprehensible fashion, but did you not understand something in my previous post?
The download (FrontMission2_PatchF-1.zip) contains a second Zip file named "Data Conversion.zip". That Zip file contains "DataConversion_Readme.txt", which tells you that it "contains two patches (in xdelta format): one for patching an original version to become identical to the reprinted versions. The other one is for patching a reprinted version to become identical to the original version." If this is not what you are trying to do, then you should not be using xdelta at all.