In an effort to use WebConfigModifications less, I am trying to move some binding redirects and safe control entries into the solution manifest. The DeploymentTarget of the assembies is GlobalAssemblyCache.
The solution is being installed using both the -GACDeployment and -AllWebApplications flags.
After making this change (and commenting out the WebConfigModifications code), the solution is in Central Admin (showing as activated on the web application), but the Web App features are not showing up in Central Admin. The web config changes are occurring as expected, and ULS confirms that I'm not starting up any of the web config timer jobs (it's a farm test)
I can access the features via Get-SPFeature, and I can confirm that they are not hidden.