Best Way to Upgrade to next OS OpenCore Mac Pro 5,1: App Store vs. USB Boot?

I’m currently running OpenCore with Big Sur, and I’m considering upgrading to Sonoma or Sequoia. Is there any difference between:

1. Downloading and installing the update through the Mac App Store, then using Post-Root Patcher to fix anything missing, or 2. Using the OpenCore USB maker and installing through the boot selector? 

I’m asking because I’ve had issues in the past with my mid-2012 Mac Pro (5,1), where the USB keyboard or mouse wouldn’t work when going through the usb is taller