Cleanup internal usage of qiskit.passmanager in qiskit.transpiler to avoid warnings

[mtreinish]

I guess until the code path really gets deprecated it doesn't really matter, but I just wanted to note that while testing the 1.0 beta I tried looking at all warnings and noticed that the

PendingDeprecationWarning: Building a flow controller with keyword arguments is going to be deprecated. Custom controllers must be explicitly instantiated and appended to the task list.

warning gets generated a lot internally by Qiskit. For instance, this code generates it:

import warnings

from qiskit import QuantumCircuit, transpile


warnings.simplefilter("default", PendingDeprecationWarning)

qc = QuantumCircuit(1, 1)
qc.measure_all()

transpile(qc, optimization_level=0)

Originally posted by @wshanks in #10127 (comment)

[mtreinish]

I think this has been closed by #11448. There's still a pending followup PR #11494 but I think the warnings flagged by this issue have already been fixed so I'm going to close this.