Flat Files for application on-boarding

Flat files or mostly known as csv files is the most common format in which applications prefer to give the data. In most of the projects, I have seen people writing a separate utility(java) which will actually validate the flat files, and convert it into a desired format before sending it for import, or store it in a custom database and read using jdbc connectors.
This design actually expedites the process of on-boarding if all teams are agreed upon a fixed format, though for the long term Identity and access management road map this files needs to be replaced with direct connectors to achieve auto provisioning and de-provisioning.
In SailPoint we have some options build in the tool to read and modify the file using rules like(build map, pre-iterate, post-iterate, File parser rule). This rules gives the flexibility of writing custom logic per application, but it requires more effort in maintenance and future enchantments.
So either having a fixed format of file or different format of file for every application, both have advantages and disadvantages, and none of the option can be picked without looking into all aspects of the enviornment.