To reproduce:
1) Download attached project
2) Test this on 5.4 with WSA installed by using command "<Unity.exe location> -batchmode -nographics -projectPath "<Path_To_Project>/CommandLineDelayCall" -executeMethod MyDelayedCall.MyMethod
Note: Don't add -quit. DelayedCall sometimes doesn't trigger if it is quit too quickly
3) Wait a bit to make sure the call is run
4) Open Editor.log - notice that both Debug.Log have been triggered
5) Repeat steps 2-4 on 5.5+ without WSA installed - nothing changes
6) Repeat steps 2-4 on 5.5+ with WSA installed - this time EditorApplication.delayCall never calls the other method

Reproduced in 5.5.0f3, 5.6.0b1
Not reproduced in 5.4.3p4