The problem is that mkusb should let you use the remaining space as an usual storage USB stick as stated in the community wiki:
The rest of the drive space is used for storage compatible with Windows
... the problem is that it doesn't, Windows 10 sees that FAT32 partition as unusable and asks me to format it. The Windows's disk management tool is not able to format it, change letter or anything else (though it correctly show me the partitions that mkusb has created in the USB drive).
I tried also on OSX and on ElementaryOS and I have no issues there, I can correctly mount, read and write in the storage partition.