Is it considered acceptable to begin sentences with "indeed" and "actually" in formal English writing?

Yes, both words may be used at the beginning of a sentence. Each of those words is a transition word, so the preceding sentence should give rise to the transition.

Ex: “This was the first time Sue ever yelled at Mary. Indeed, it was the first time anyone could remember her raising her voice in anger at all.”

Ex2: “The Romans thought they had routed the Parthians. Actually, the Parthians were only feigning retreat to lure the Romans away from their defenses in order to tire them and then ambush them.”