Joseph
” Do you think any Halachas that the Shulchan Aruch”
sure. There are plenty. Though we may follow the Rema, or shach tc.
As to the OP the examples you list arent really “mitzvos”
Though thereare soem that we dont practice some have better answers than others
Hilchos yerusha, we basically dont follow. that ist to say we dont follow halacha ch”v, its that we ignore the actual halacha, and instead use a shtar chatzi zachar give girls inheritence.
Tzaraas, is one that doesnt have a clear answer, as to why someone with a white spot, doesnt go to a Koehin, which is a mitzvah deoraysah.
PArah Adumah feels “bais hamikdashi” so we just assume that it is tied to the bais hamikdash, but it sint really