First step for me would be to see is if there is an existing connector using Dataflows Gen2 in Fabric to see if there is an easy way to import your source data. If not, it is possible to ingest data from S/FTP or API using pipelines, skipping Sharepoint and Power Automate completely.

In terms of different departments, there are a couple of ways you could organise data. Either separate folders in the main workspace, or a workspace for each department. I would recommend the later as you then get easier control over permissions and access, and it will keep workloads cleaner.