To reproduce:
0) Make sure you have both Win Standalone and WebGL platforms installed
1) Create a new project
2) Open Player Settings
3) Change the Win Standalone Scripting Backend to IL2CPP

Expected: There's "C++ Compiler Configuration" selection with three options (Debug/Release/Master)

4) Switch to WebGL platform

Actual: There's no such selection as for Win Standalone

Reproduced in 2018.3.0b9

Workaround: This can be added by manually editing ProjectSettings file

il2cppCompilerConfiguration:
WebGL: 2