SQL Job Step timeout If a SQL Agent job step executing a stored procedure on a linked server times out,  does the agent kill the SPID on the linked server or does it continue to run on the linked server?
Whenever a client disconnects from SQL Server, the database engine rolls-back any open transactions prior to the spid terminating.

This applies to all clients, even a "client" Agent Job running via a linked server.

If a stored procedure running via a linked server times out, the connection to the target server will disconnect, causing all open transactions in that session to roll back.

This answer shows many of the ways an open transaction can be rolled back.