This is probably a question just for linguists. Is there a reason why verbs with Usted are conjugated the same way as with El and Ella? A historical reason maybe?
"Usted" derives from "Vuestra Merced" and is therefore conjugated in the third person, as a way to show respect.
It would be similar to Your Majesty (Su Majestad) and Your Excellency (Su Excelencia), which are also conjugated in the third person even if the person holding that high rank is being directly addressed.
You can see, among others, this source.
They are conjugated the same way because they are all third-person pronouns.
Let me explain. Usted comes from an evolved and adapted form of Latin's "vuestra merced" (your grace). We're talking about a handful of centuries worth of changes too! Your Grace is a third-person pronoun that expresses praise to the listener, grace even!
Just like today how we shorten longer words to suit our needs, or we say it differently because it's easier to get off the tongue, the word was bastardized to the point we know it as today.
Here's a good read on it all.
As explained in usted and its usage
Usted is grammatically third person singular, such a use is called honorific third person [...] Obviously being grammatical 3rd person singular means that the verbs need to be conjugated as 3rd person singular. Also all pronouns must be 3rd person. see Vartec's answer
Vuestra merced (a really antique way to say something like your highness) evolved to usted.
Vuestra merced --> Vusted --> usted
Also, in Why is “Usted” grammatically a third person? is is explained that
Since [Your grace] was an indirect way of addressing someone, it was inflected in the third person.