Yes, I did boot the Home Menu before but it didn't work with new Citra build (I use the same file each time), you need an older Citra Build (unfortunately, I delete this build but I think it's before March 2016).
You can't access the Home Menu through System Settings App (System Setting App is not the Home Menu).
I mean if you find a way to bypass 3D slider configuration and you complete your settings, you'll have a black screen because there is no Home Menu.
I dump my 4.5 EUR nand, extract a file called 0004003000009802.cia (this is the Home Menu) and decrypt it with Decrypt9 (Cia Decryption Deep) with my old 3DS. Then I convert .cia to .3ds manually with Ctrtool and it worked.
Edit : I heard that Citra can now read .cia file directly (the file has to be decrypted anyway), I will test it later and check if it works.