Because the attributable earnings must be calculated over the investment performance of the entire account, unless all of the money in the Roth IRA was invested in the same investment, an in-kind movement to the traditional IRA of exactly the same shares as were purchased with the $6,000 excess contribution would likely not meet the requirements of a recharacterization that would correct the excess Roth IRA contribution. However, if the brokerage calculated the attributable earnings over the investment performance of the entire account and then did an in-kind transfer of a number of shares having a total value on the date of the transfer equal to $6,000 plus the calculated gain (or loss), that would satisfy the requirements of CFR 1.408-11.
In your case, the $100 gain would need to have been determined based on the overall investment performance in the Roth IRA, not just the performance of the shares that were moved in the in-kind transfer to the traditional IRA. Done as an in-kind transfer, the transfer would then have to consist of any shares from the Roth IRA having a value of $6,100 on the date of the transfer.
