It can install it in the same way...however it will do what you tell it to do.
If you tell it to install a policy and don't give it installation targets, it will default to how that policy is configured in regards to installation targets.
Scenario: Provider-1 Domain with 3 clusters and a separate policy for each cluster.
Policy-A is configured with installation targets of Cluster-A
Policy-B is configured with installation targets of Cluster-B
Policy-C was just built and is for Cluster-C however it is not completely configured and has a Any for installation targets.
In fact, Cluster-C hasn't even been built yet, an Engineer is just working on the policy to get it ready.
Manually with Smart Console if you attempt to install Policy-C on Cluster-A or Cluster-B it will pop up a warning saying are you sure? The policy doesn't match what is installed...yada...yada
From Smart Domain Manager doing the re-assign w/ install for the whole domain would just install Policy-A and Policy-B and would ignore Policy-C.
For API, if you pull the list of packages and tell the API to install all available packages, it would Policy-A on Cluster-A. Policy-B on Cluster-B and Policy-C would install on both Cluster-A and Cluster-B and be happy about it.
Lots of power, but it will also let you shoot yourself in the foot