To reproduce:
1) Download attached project
2) Run Unity through command line like this: '<Path_to_Unity>/Unity.exe -batchmode -nographics -projectPath "<path_to_project>" -buildTarget win32 -quit'
3) Check Editor.log - notice that Editor ran well and didn't crash
4) Run the same command like in Step 2, but change -buildTarget to something else, like 'android' or 'linux'
5) Check Editor.log - it crashed

Reproduced in 5.5.0b11, 5.5.0f3, 5.5.0p1, 5.6.0b2
Not reproduced in 5.4.0f3, 5.4.3p4, 5.5.0b1, 5.5.0b5, 5.5.0b8, 5.5.0b9, 5.5.0b10