I managed to obtain this, check:
rotation working as desired
Note: The green and the red views are subviews of the controller's view. The blue view is subview of the red view.
Idea
According to https://developer.apple.com/library/archive/qa/qa1890/_index.html, we need to apply an inverse rotation to the view when it is transitioning to a new size.
In addition to that, we need to adjust the constraints after rotation (landscape/portrait).
Implementation
class MyViewController: UIViewController {
    var viewThatShouldNotRotate = UIView()
    var view2 = UIView()
    var insiderView = UIView()
    var portraitConstraints: [NSLayoutConstraint]!
    var landscapeConstraints: [NSLayoutConstraint]!
    override func viewDidLoad() {
        super.viewDidLoad()
        viewThatShouldNotRotate.backgroundColor = .red
        view2.backgroundColor = .green
        insiderView.backgroundColor = .blue
        view.addSubview(viewThatShouldNotRotate)
        view.addSubview(view2)
        viewThatShouldNotRotate.addSubview(insiderView)
        portraitConstraints = createConstraintsForPortrait()
        landscapeConstraints = createConstraintsForLandscape()
    }
    func createConstraintsForLandscape() -> [NSLayoutConstraint] {
        return NSLayoutConstraint.autoCreateConstraintsWithoutInstalling {
            viewThatShouldNotRotate.autoMatch(.height, to: .width, of: view)
            viewThatShouldNotRotate.autoMatch(.width, to: .height, of: view)
            viewThatShouldNotRotate.autoCenterInSuperview()
            view2.autoPinEdgesToSuperviewEdges(with: UIEdgeInsets(), excludingEdge: .top)
            view2.autoSetDimension(.height, toSize: 100)
            insiderView.autoPinEdges(toSuperviewMarginsExcludingEdge: .bottom)
            insiderView.autoSetDimension(.height, toSize: 100)
        }
    }
    func createConstraintsForPortrait() -> [NSLayoutConstraint] {
        return NSLayoutConstraint.autoCreateConstraintsWithoutInstalling {
            viewThatShouldNotRotate.autoMatch(.height, to: .height, of: view)
            viewThatShouldNotRotate.autoMatch(.width, to: .width, of: view)
            viewThatShouldNotRotate.autoCenterInSuperview()
            view2.autoPinEdges(toSuperviewMarginsExcludingEdge: .top)
            view2.autoSetDimension(.height, toSize: 100)
            insiderView.autoPinEdges(toSuperviewMarginsExcludingEdge: .bottom)
            insiderView.autoSetDimension(.height, toSize: 100)
        }
    }
    override func viewDidLayoutSubviews() {
        super.viewDidLayoutSubviews()
        if view.bounds.size.width > view.bounds.size.height {
            // landscape
            portraitConstraints.forEach {$0.autoRemove()}
            landscapeConstraints.forEach { $0.autoInstall() }
        } else {
            landscapeConstraints.forEach {$0.autoRemove()}
            portraitConstraints.forEach { $0.autoInstall() }
        }
    }
    override func viewWillTransition(to size: CGSize, with coordinator: UIViewControllerTransitionCoordinator) {
        super.viewWillTransition(to: size, with: coordinator)
        let viewToRotate: UIView = viewThatShouldNotRotate
        coordinator.animate(alongsideTransition: { (UIViewControllerTransitionCoordinatorContext) -> Void in
            let deltaTransform = coordinator.targetTransform
            let deltaAngle = atan2f(Float(deltaTransform.b), Float(deltaTransform.a))
            var currentRotation = (viewToRotate.layer.value(forKeyPath: "transform.rotation.z") as! NSNumber).floatValue
            // Adding a small value to the rotation angle forces the animation to occur in a the desired direction, preventing an issue where the view would appear to rotate 2PI radians during a rotation from LandscapeRight -> LandscapeLeft.
            currentRotation = currentRotation + (-1 * Float(deltaAngle)) + 0.0001
            viewToRotate.layer.setValue(currentRotation, forKeyPath:"transform.rotation.z")
        }) { (UIViewControllerTransitionCoordinatorContext) -> Void in
            var currentTransform = viewToRotate.transform;
            currentTransform.a = round(currentTransform.a);
            currentTransform.b = round(currentTransform.b);
            currentTransform.c = round(currentTransform.c);
            currentTransform.d = round(currentTransform.d);
            viewToRotate.transform = currentTransform;
        }
    }
}