@Nomelas
from what little bit i know of wiiflow and cios i believe the reason your method works is because not only are you using beta53 alt but because following the guide you chose to follow it uses ios58 as the base and installs it in slot 251. so in slot 251 is d2x[58] v10 beta53 alt.
In slot 249 is base 56 and 250 is base 57.
when you start wiiflow with force cios on and cios set to 251 then wiiflow will use that cios for all its input/output. if you have your wii game's config ios setting set to 'auto' then those games will also use the cios in slot 251 unless the game wants to use IOS57 then wiiflow makes that game use slot 250 because it's base 57.
if you have your wii game's config ios setting set to a specific cios then the game will use that cios.
not sure why you have to have wiiflow and nintendont on both SD 'and' USB. but i'm curious, do you have data_on_usb set to yes in wiiflow.ini or wiiflow_lite.ini? which means you would need your wiiflow folder with all the settings, covers, plugins, themes, etc... on your USB HDD.
here's my guess at getting usbloader gx to work with your setup - you need to set usbloader gx the loader itself set to use cIOS 251 as well as the global IOS setting for all wii games set to use 251.