To answer my own question, just in case people are looking for this exact answer, yes the funds will be properly direct deposited into your bank account. So filing with TurboTax and having the fee for the filing subtracted from your federal return, meaning it goes thru a 3rd party, doesn't seem to have affected the IRS properly sending you your stimulus check via direct deposit. As I have replied to others asking the same thing, I am a sample size of one but it is a good sign nonetheless.
