The difference is taxable,
Wrong. The result of a rollover of the entire amount of any distribution (other than a rollover from a traditional account to a Roth account), in-kind or not, produces the same taxable result as if the distribution never happened. The difference between the share value at the time of the distribution and the time of the rollover contribution is not taxable because the same "property" is rolled over.
Ignoring the 0.001 share difference, you rolled over all of the property distributed, so none of the distribution is taxable. To do this in TurboTax, you indicate that dollar amount rolled over was the dollar value of the shares as valued on the date of the distribution, not the dollar value of the share on the date of the rollover contribution, that the difference in share value is not included on Form 1040 line 4b or 5b. Your tax return must then be printed and mailed along with your explanation statement saying that this was a rollover of the same shares that were distributed in-kind.
Taking into account the 0.001 share difference, I'll assume that the 0.001 share difference means that you rolled over 0.001 share less than was distributed since it's impermissible to roll over 0.001 share more than was distributed. To calculate the exact dollar value rolled over, multiply the per-share value of the shares on the date of distribution by the number of shares actually rolled over. If the per-share value was low enough on the date of distribution, the 0.001 share lower amount rolled over will still be the same dollar value when the dollar value is rounded to the nearest dollar.
As I think I said previously, there's a good chance that brokerage's cost-basis tracking of non-covered shares will be inaccurate, but since they don't report to the IRS the cost basis of the sale of non-covered shares, it's always your responsibility to track the cost basis of non-covered shares. Your cost basis in non-covered shares ends up being unchanged by an in-kind distribution followed by a rollover of all of the same shares.
