Hi @geeday !
Thanks for the details 
Very nice. I hope you are using Torizon for this 
Do you absolutely need to use USB stick? You could use e.g. TFTP/NFS/DHCP to boot your module from the network. IMHO, this method makes things even easier than using USB stick. Not long ago, I was providing help about this in this other thread: NFS -: server not responding, still trying -upstream-Tezi_7.x - iMx6 - #6 by henrique.tx.
What I did there was on a Reference Image of Toradex BSP. But it might help you as well, since I suppose you are on Torizon OS (which gives you OTA capabilities out-of-the-box).
Totally agree with you. 
Best regards,