Although tested on LEAP 15, I remember this was once a problem on 42.3 (haven't
checked whether the problem has returned on 42.3)

No matter the background and icon combination, when an object (eg text file) is
created in the Desktop directory, on the Desktop the icon disappears into the
background because the icon is set to "transparent"

This seems to apply even in different backgrounds, no matter whether the
background is light, dark, with image or solid color... Unknown whether the
icons themselves are created incorrectly with transparency set (I would think
should not) or a transparency setting is set incorrectly in theme rendering.

Should be easy to re-produce.
Any way creating an object in the Desktop directory should be sufficient, eg

touch ~/Desktop/New_file

Then look for what you just created,
It should be vaguely visible in the top left of the Desktop.