Historically, NetApp had recommended that flow control be disabled on all network ports within a NetApp Data ONTAP cluster. This approach is no longer the case. Guidance in this area has since changed, and the new recommended best practice is as follows:
• Disable flow control on cluster network ports in the Data ONTAP cluster.
• Flow control on the remaining network ports (the ports that provide data, management, and intercluster connectivity) should be configured to match the settings within the rest of your environment.
In short, Flow control setting should be the same end-2-end. (Either disable it or set the fixed speed, but do not let it auto-negotiate).
I don't know how VM's CPU usage could be affected by this, haven't come across it. Throughput could be an issue .