I looked at the code and it sems the philosphy is that you can plug several settings source implementations, the one Nicolas did is file based.
So I think it is not incompatible with the file-provider-plugin as we probably need an implementation for file-provider-plugin as it allow settings sharing between jobs.
So I suggest the following:
1) I send a pull request to file-provider-plugin to support toolchains config files
2) I send another pull request to jenkins (maven plugin) to handle those toolchains config files
3) I will open a JIRA to support file-provider plugin the new way, adding a new implementation, and adding toolchains support as well (btw, it seems nicolas's work is not complete as it does not support global settings and I don't know if it is merged in master)