1 pointI think those are fine concerns. One thing that Alex and Christopher has said before is that 1) Covecube isn't in any danger of shutting down any time soon and 2) if it would, they would release a tool to convert the chunks on your cloud storage back to native files. So as long as you had access to retrieve the individual chunks from your storage, you'd be able to convert it. But, ultimately, there aren't any guarantees in life. It's just a risk we take by relying on cloud storage solutions.
1 pointThere is ABSOLUTELY NO ISSUE using either the built in defragmentation software, or using 3rd party software. Specifically, StableBit DrivePool stores the files on normal NTFS volumes. We don't do anything "weird" that would break defragmentation. At all. In fact, I personally use PerfectDisk on my server (which has 12 HDDs), and have never had an issue with it.