I have lots of problems with make disk BUT if you install a pure DOS partition then MAKEDISK work 100%. I have never had a problem since I did this.
You could also download GEMULATOR 2000 and access the disk direct from that and copy file to the hard disk.
There was also a programon the ST that added the byte or two to the bootstrap of the floppy so that PCs could read them - so no more help there nor can I remember how could it was.