So, after a year and a half, I was able to figure out how to avoid this problem.
Let’s look at this step by step:
1. Create simple object (mostly this bug appears in spherical shapes)
2. Create custom mapping (I’ve unwrapped objects by cutting it every seam)
3. Create custom mesh and export it
4. Import back this mesh and check UV mapping
Now, you can see the problem.
From this point starts most interesting things…
I’ve noticed, that created UV island not matching mesh shape (before exporting).
So, I’ve decided to setup mesh settings in the preferences first.
Then you need to recreate your UV mapping and export mesh (this is important) with the same settings as the settings in the properties.
In the end we can have perfect UV map:
Summarizing all the above:
before we create our custom UV mapping we need to setup custom Render Mesh Quality in the Preferences and after that we need to create or export mesh with the SAME SETTINGS as the Render Mesh Quality settings in the preferences. After that no UV problem will be appears. Mesh displayed in the UV map should be identical with the export mesh.