I'm not sure what you mean by "recover the extra 50% tax." TurboTax asks two different RMD questions for different purposes. My comment refers to the immediate RMD question that TurboTax asks for each individual Form 1099-R entered where TurboTax is trying to determine the amount of the distribution that is eligible for rollover, and no part of the regular pension payments to you is eligible for rollover. If you are instead referring to the question that appears after clicking the Continue button on the Your 1099-R Entries page and asks if you satisfied all of your RMDs (for the purpose of calculating an excess-accumulation penalty on Form 5329 Part IX), I would probably not include anything related a late pension or annuity payments in response to that question. Pension and annuities that make periodic payments do not have a year-end balance on which to calculate a non-periodic RMD amount, so there's really no way to properly include them on Form 5329 Part IX, so there is probably no need to request a penalty waiver for having received a regular pension payment late.
Keep in mind, "pension" generally refers to regular periodic payments received for life, essentially the same as a qualified annuity. Any portion of a retirement plans that permits non-periodic distributions (other than a pension buy-out) would not be referred to as a pension plan and certainly is subject to RMDs calculated on the previous year's year-end balance and the age of the participant.