To reproduce:
1. Open users attached project "zTest.zip"
2. Open "SampleScene.unity" scene
3. Move the blue cube around
4. Observe as one of the white points is visible through the cube

Expected result: both points are not visible through the cube
Actual result: the point that is using Handles.DotCap function which is obsolete is not visible (correct), but the one with the new function Handles.DotHandleCap can be seen through the cube (incorrect)

Reproduced on:
2017.2.3p1 2017.3.2f1 2017.4.6f1 2018.1.7f1 2018.2.0b11 2018.3.0a3

Notes:
The user has found in the source code that DotCap uses the zTest : HandleUtility.ApplyWireMaterial(Handles.zTest);
And DotHandleCap does not use the zTest: HandleUtility.ApplyWireMaterial();

More info: https://forum.unity.com/threads/handles-dothandlecap-ztest-issue.535437/

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Fixed in 20018.3a06.