Does FME Server have an option for an ETA of how long a job will take to run?

There's so many unknowns in an FME process. The outputs of a single transformer will effect the next one which will effect the next one and so on. A slight change in the input dataset could have a massive effect on any of the transformers in the process.

In comparision, a file copy is simple. Theres 100gb of files, and transferring them at 500mb/s, therefore this will take ~ 3.5mins.

Unfortunately not, although with the job metrics (introduced in FME Server 2021) it does maintain statistics. In the workspaces list it'll show you the average processing time for that particular workspace. Of course this depends wildly on a lot of factors, but at least it's something.