I can see that the ILMergeConfig.json is hard coded as a configuration file here:
https://github.com/emerbrito/ILMerge-MSBuild-Task/blob/master/ILMerge.MSBuild.Task/ILMerge.MSBuild.Task/build/ILMerge.MSBuild.Task.targets#L28
Would it be possible to change this to a variable that just has this by default as "ILMergeConfig.json" but it could potentially be set in the main csproj to be a different file? The reason is because we have a few different build configurations and are cross targeting so need a different ILMergeConfig.json per build configuration. Happy to help if this is possible