I'd expect making the copy take longer is more stressful to a drive than writing the data as quickly as possible while the drive is already spinning and the heads are already where the data needs to go. Is there any science behind that idea we can look at to change my mind?
Speed throttling is only an option with FTP transfers at this time.
Appending is also an option with FTP, where transfers are often interrupted and need to be resumed. It almost never makes sense, and can be dangerous if misused, on local or network-drive file copies, so we don't offer it for them. Why do you find yourself needing it?
Opus has a few ways to replace files based on date, size or content but I don't think we currently have one for the size being smaller (only different). Updated files are often smaller than old ones (or vice versa) so it's rarely a criteria people need, at least in our experience. It could be done using scripting, however.
By the way, it's better to ask one question per post unless things are closely related (see the FAQ about this for our reasoning).