This seems like a big enough "platform" difference that we should be testing in platform ci.
To do that you would need to add another item in the matrix here
https://github.com/tianocore/edk2/blob/master/EmulatorPkg/PlatformCI/.azurepipelines/Windows-VS2019.yml#L26
and here:
https://github.com/tianocore/edk2/blob/master/EmulatorPkg/PlatformCI/.azurepipelines/Ubuntu-GCC5.yml#L25
An example in OVMF of how this is done is here
https://github.com/tianocore/edk2/blob/master/OvmfPkg/PlatformCI/.azurepipelines/Windows-VS2019.yml#L95