To reproduce:
1. Open the project folder and open the "native.dll.meta" file in Assets/Plugins/x86_64
2. Check the value of Win64->settings->CPU, it should be None
3. Open "DllTest.zip" project in Unity editor
4. Click the "native" file in Assets/Plugins/x86_64 and check the inspector.
5. In the "standalone setting" tab of "Platform settings", both x86 and x86_64 is checked. (But if build for windows standalone, the native.dll is not copied to Plugin folder.)

Expected result: information in Inspector and in metafile is the same.
Actual result: it's not the same. Inspector shows "x86_x64" checked, when in metafile it's "None".

Reproducible: 5.5.3p4, 5.6.1p1, 2017.1.0b7, 2017.2.0a1
Not reproducible with 5.4, because there are no "Platform Settings".

Workaround:
Uncheck the x86_64 and check again, apply. The meta file changes the value from None to AnyCPU.
Build again, "native.dll" is included in standalone's Plugin folder.