To reproduce:
1) Open attached project
2) Try building it on WebGL

Expected: It builds normally, as both plugins are excluded
Actual: Build fails with error that two DLLs are colliding

Workaround:
3) Search for sqlite.dll
4) Pick one of them
5) Instead of Including "Any Platform" -WebGL, Disable Any Platform, and Include all platforms except for WebGL
6) Do the same for other dll too
7) Build again

This time, it builds properly

Reproduced in 5.5.0f3, 5.6.0b11, 2017.1.0a2
In 5.4, you cannot do "Any Platform" -something, but doing the workaround works as expected