I just tested this myself on a lab system, going from 8.1.4.40 (VM NA) to 8.2.4.42 using the Firmware Upgrade wizard.
I DID see the timeout error at the end of the wizard (after roughly 18 minutes for me, combined with the download and script execution), but the gateway was upgraded and restarted as expected.
Make sure your "Set Configuration" is for SCP and type Script for both Firmware and Configuration MIB settings, with "Extreme Control Upgrade - SCP" as the type.
There are some hard-coded timeouts in the upgrade script that will exit the script in various "error" states if certain return values aren't sent, but most should not be catastrophic.
As a workaround, you can always download/copy the nac_appliance_64bit_sw_upgrade_to_8.2.4.42.bin file (or analytics upgrade binary) directly to the engine, chmod it and execute it directly on the engine if all else fails.