My answers:
1) Hardware changes are assumed by the Managed Instance server inmediately after scale up has finished. It is reconfigured accordingly.
2) I have seen customers messed up things on Managed Instance, but after a scale up/down the things that they messed up got repaired.
3) The scaling operation of storage could take a while depending on the amount of data you have across all databases in the Managed Instance. Scaling up/down usually takes 5 minutes but here you will find the duration of other managed instance operations.
4) The scaling operation from Standard to Premium can take 2.5 hours. This invloves a downtime and a rollback of any transactions in progress.