Hello,
the Pause button tries to do the appropriate thing. What's appropriate depends very much on the transfer protocol used. Some transfers can be stopped and resumed, others can only be lowered in transfer rate. Others have to finish up a chunk and can then wait until the job is no longer paused.
Rebooting is the same as canceling a profile. It has to start over with building the file list and then copying remaining files.
Interrupted large file transfers can only resume with local drives, network drives, and FTP and SSH/SFTP. All other protocols have to re-copy a big file from the start.