Are Mac and Windows version Scapple files compatible

Yes, that is exactly what this problem will look like if you have notes that are very close together. They can end up overlapping each other or weirdly word-wrapping when you switch platforms. That’s mainly because the height of the box is not fixed, but determined by the text content (otherwise text would crop out of view).

You don’t need much extra space though, I’m only talking what it takes to display the note on both platforms without the text content changing the size of the box. That may be as small as a few pixels in some cases, and you may find some fonts work better than others in this regard.