My team were experiencing these issues intermittently with long running SSIS packages. This has been happening since Windows server patching.
Our SSIS and SQL servers are on separate VM servers.
Working with our Wintel Servers team we rebooted both servers and for the moment, the problem appears to have gone away.
The engineer has said that they're unsure if the issue is the patches or new VMTools that they updated at the same time. We'll monitor for now and if the timeout problems recur, they'll try rolling back the VMXNET3 driver, first, then if that doesn't work, take off the June Rollup patches.
So for us the issue is nothing to do with our SQL Queries (we're loading billions of new rows so it has to be long running).