Download on PC and transfer to sd. What's so hard about that. Freeshops and the Qr installation methods are slow has hell to download and sometimes they could fail half way through the download process
if you have a n3ds, you can reenable the ftp option with smb 1.0 and I think it requires a second option which I've forgotten. it's pretty good from what I remember back on windows 7. it's disabled by default on windows 10 and probably 11.
If you have a normal router, it isn't slower than it is downloading games from the eShop on your console - or that shop clone you mentioned.
If you were expecting for something faster, besides using custom-install inserting your SD card into your PC, there's no other option. I would say custom-install is the best option ever anyway, it's not like you'll install games everyday for the rest of your life.