I played with this and found a hacker way to get rid of them. I am not 100% sure that this will work in all cases, but it can be.
After reading Area.transform, JavaDoc mentions
Transforms the geometry of this Region using the specified AffineTransform. The geometry is transformed into a place, which constantly changes the closed region defined by this object.
I had a hunch and added the ability to rotate the Area by holding the key. As the Area rotates, the “inner” edges began to slowly disappear until only the outline remained. I suspect that the “inner” edges are actually two edges very close to each other (therefore, they look like one edge), and that the rotation of the Region causes very small rounding errors, so the rotating view “fuses” them together.
Then I added code to rotate the area in very small steps for a full circle when a key is pressed, and it looks like artifacts disappear:

The image on the left is an area built of 10 different random triangles (I increased the number of triangles to get “glitches” of the areas more often), and on the right - the same Area, after it was completely rotated 360 degrees with a very small step (10,000 steps).
Here is the part of the code for turning the area in small steps (in most cases there will be less than 10,000 steps):
final int STEPS = 10000;
As I said, I'm not sure if this works in all cases, and the number of steps required can be much less or more depending on the scenario. YMMV.
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