came and overshadowed

"appeared and covered"

Then a voice came out of the cloud

Here "a voice came out" is a metonym for someone speaking. It can also be stated clearly who spoke. AT: "Then someone spoke from the cloud" or "Then God spoke from the cloud" (See: rc://en/ta/man/translate/figs-metonymy and rc://en/ta/man/translate/figs-explicit)

God the Father expresses his love for his "beloved Son," the Son of God.

This is an important title for Jesus, the Son of God. (See: rc://en/ta/man/translate/guidelines-sonofgodprinciples)

Here "they" refers to Peter, James, and John.