Invoke() runs the current command list, but it does not clear that list afterward. So each call in the example keeps appending to the same PSCommand.

By the time result1 is invoked, the pipeline is effectively:

Set-ExecutionPolicy -Scope Process -ExecutionPolicy RemoteSigned | Get-PhysicalDisk

Set-ExecutionPolicy writes no objects to the success stream, so the appended command produces no output in this pipeline. After the first invocation, ps.Commands.Commands.Count is still 1; after adding Get-PhysicalDisk, it is 2.

Clear the command list before building the next invocation:

using var ps = PowerShell.Create();

ps.AddCommand("Set-ExecutionPolicy")
  .AddParameter("Scope", "Process")
  .AddParameter("ExecutionPolicy", "RemoteSigned")
  .Invoke();

ps.Commands.Clear();

Collection<PSObject> result1 = ps.AddCommand("Get-PhysicalDisk")
                                         .Invoke();

ps.Commands.Clear();

Collection<PSObject> result2 = ps.AddScript("Get-PhysicalDisk")
                                        .Invoke();

With the clears in place, both variants should return the disks. The difference you are seeing is therefore not command lookup or Get-PhysicalDisk behaving differently under AddCommand; it comes from reusing the accumulated pipeline.

If the intention is to execute both operations in one invocation without piping the first into the second, AddStatement() is the other option:

Collection<PSObject> result = ps
    .AddCommand("Set-ExecutionPolicy")
    .AddParameter("Scope", "Process")
    .AddParameter("ExecutionPolicy", "RemoteSigned")
    .AddStatement()
    .AddCommand("Get-PhysicalDisk")
    .Invoke();