Will my Federal Refund be $2379 instead of $2271 since I paid my Pa Taxes from my Checking Account on 3/4/19

Did you have the TT fees deducted form the Federal refund?

No.  Paid from my checking account

If you did not elect to have your fees deducted from your Federal refund, then if approved, the full amount on Line 20 of your Form 1040 will be direct deposited into your checking account.