Yes the IRS does accept certified mail.
I have sent my tax returns to the IRS through certified mail for around 5 years now and they've always accepted the certified mail at the IRS.
The IRS wants your tax return and it does not matter how you send it as long as you get it sent to them.
The certified mail will give you proof that the tax return was delivered to the IRS.
You can send your tax return to the IRS through regular mail which is usually not a problem or certified mail which makes sure they get it and you get proof they get it.
I had a tax return get lost in the mail before and it was a headache dealing with that so now I send all my tax returns off through certified mail and they've always accepted it just fine.