Quote: Just to be clear 'el' (with an accent) never means 'it' but always 'he'?
As with most things in Spanish grammar, it is rarely wise to say "never" or "always" "él" WITH an accent is used as an object of a preposition pronoun meaning "it" when it substitutes for a masculine noun.
Example (from context.reverso.net
Este pequeño inflador viene gratis con él.
Look, this little pump comes free with it.
As noted in another response él with an accent can sometimes mean "him"
It shouldn't give "i" as a possibility, but assuming you meant "it"....
It gives "it begins" as a possibility because DL is giving you possible translations for comienza in a vacuum. Without any context, comienza can translate to (he/she/it/you(formal) begins. DL is not translating the entire sentence for you, it is only giving you all the possible translations for comienza. You must now use what you have learned to pick the correct translation that fits the context of this sentence.
In this sentence, we are given the subject pronoun él (he). This eliminates all choices for comienza besides "He begins".
Él is the third-person singular pronoun (usually subjective or prepositional object) for both male persons and masculine words that do not refer to persons. "It" should be an acceptable answer. Él does not exclusively refer to people (he or him in English).
If I wanted to say "El programa comienza hoy," but I wanted to turn "el programa" into a pronoun for brevity, I would use "Él"; there is no other pronoun that I would use. ("Ello" is very rarely used; I'm not sure when, if ever in normal conversation, it would be used.)