Freeze is really meant to be a plain simple file transfer client, although it has some "helper features" like compare mode which shows differences between a vault's inventory and a local folder and the highlighting of duplicates.
But it is not meant to be a replacement for a full featured backup solution like Arq. I think some people like it a bit more "low-level" and simple and that's what Freeze is for.
Yes, Freeze uses multipart uploads with 16 MB chunks. Resuming multipart uploads works chunk-wise, for example when you've uploaded 20 MB and then the connection drops, the upload then continues at chunk number 2. When you see that an upload restarts from scratch, then the connection was probably interrupted while trying to upload the first 16 MB.
About automatic retries: Freeze automatically retries 3 times and then you have retry manually.
For unreliable and slow internet connection I recommend setting max. parallel uploads to 1 and disabling the upload speed limit.
I plan make the chunk size configurable for a future update. I makes sense to use a smaller upload chunk size for unreliable internet connections.
It's actually not too hard to calculate the storage costs and it's really cheap. I've been using Glacier for backups since the service has been launched. The calculation of the retrieval costs are a bit tricky though. But if you use Glacier for disaster recovery only, it shouldn't matter too much.
Freeze has no encryption or compression features built-in, so you are responsible to prepare the data as you want it to be stored on Glacier before you upload it.
I don't like built-in encryption features in file transfer or backup apps too much, because they are often proprietary and that may make it hard to switch to another client.
As a workflow example, I personally encrypt my archives with gnupg and store them on external hard drives and additionally upload them to Glacier for disaster recovery.
Another possible thought for the roadmap would be some sort of pluggable architecture for encryption. Let third-parties develop open encryption plugins that this runs inside prior to uploading.
Arq is a full featured backup solution. Freeze on the other hand is not really meant to be a backup solution, it's rather a file transfer client for Glacier where you get a raw view on your vault's inventories with upload/download features.
But it is not meant to be a replacement for a full featured backup solution like Arq. I think some people like it a bit more "low-level" and simple and that's what Freeze is for.