I'm not entirely clear about the whole picture of the workflow. Just some thoughts:
1. Must the tool be a web tool? From what was described, a local script tool would be sufficient to meet your needs, and it can work with a local file path.
2. Consider downloading the data onto server for processing (i.e. the script tool will use a server path). Do the users need to access the output file gdb? If so, find a way to allow them to download e.g. by copying it to a shared network drive or uploading it to portal for users to download.
3. I sensed that the ultimate concern here is on service performance if such processes were carried out online. Have you maybe looked into optimizing service performance? That would address your root concern.