Replace usage of Isometry3<T> by RigidTransform<T> to simplify code

[agalbachicar]

Isometry has been deprecated in favor of RigidTransform because of familiar semantics with roboticists and enhanced checks in rotation matrices for robotic use cases.

After maliput/drake_vendor#14, and as part of https://github.com/ToyotaResearchInstitute/delphyne/pull/701/files code is a bit verbose because of keeping the Isometry3 in the interface. We should replace the Isometry3 by RigidTransform in places where it is consumed.