The time machine has be doing a voluntary RRSP withdrawal next year for ~24k and the estimated tax owing $1088. 

As far as I know, WealthSimple does not charge a fee for for withdrawing money from an RRSP (but I know other Brokers do), so I can structure my withdrawals to what works best.

CRA stipulates 10% withholding on amounts up to $5000, 20% for 5k to 15k, and 30% for over 15k.

So even if I do multiple withdrawals for less than 5k, there will still be 10% withheld - ~$2400

Are these withholding rates used in any of the MRA/Time Machine calculations? If not, what is the best way to account for these and the subsequent tax refund?

You can enter the withholding taxes you’ve already paid in the current year for the TIME MACHINE to credit them to you (this is information from your RRSP provider). You'll see a tax refund in the TIME MACHINE's year report when applicable; it will be paid on Dec 31. For future years, the TIME MACHINE only has a resolution of one year and it closes the books each Dec 31st. Any withholding is essentially immediately credited to taxes, and you won’t see it in the cash flow. In real life, there is a few months' delay between the payment of withholding and when you get the refund, but that shouldn’t matter much for long-term projections.