If you execute the FPD upgrade with 6.1.x, it will complete significantly faster than if you execute it on 5.3.x. This is due to improvements made in 6.x.x. You can read mode about this in BRKSPG-2904 from Berlin 2017 or Las Vegas 2016.
In addition to that, if you run the FPD upgrade with 5.3.x, some cards may reach a timeout (see https://supportforums.cisco.com/document/13116771/fpd-101-asr9k-platform).
/Aleksandar