If there is no cash distributed, there can be no tax withholding.
Quarterly estimated tax payments can be made by check using IRS Form 1040-ES or you can use IRS Direct Pay:
https://www.irs.gov/payments/direct-pay
Except for possible transaction fees and changes in share value during the process, distributing shares in-kind is generally no different that selling the shares in the IRA, distributing the cash and using cash to repurchase the shares outside the IRA. This would allow for tax withholding and substituting other funds to make the repurchase, potentially a better alternative than making an estimated tax payment due to the difference in the way that withholding and estimated payments are allocated by tax quarter.
