That is an interesting letter ruling, but it does not specifically address selling short stock in an IRA. The ruling is about a charitable remainder trust.
It is relevant in the sense that the IRS appears to support the idea that borrowing stock is not a form of "indebtedness," as that term is used in a very specific context in the law, and it also supports the position that income derived from the short sale of stock is not "unrelated business income."
But the ruling does not discuss IRAs at all.
My guess is that most, if not all brokers, simply will not allow shorting stock in an IRA because it requires a margin account, and there is a general rule that you cannot use assets in an IRA as collateral for a loan. Even if borrowing stock is not a prohibited loan, the brokers simply don't want to set up an account that has margin capabilities in an IRA.
Plus there is the risk of a margin call if the shorted stock rises, which can create a real nightmare. Meeting the margin call by depositing additional money could result in excess contributions. But if don't meet the margin call, and the broker liquidates the position, you could have a negative balance. Curing the negative balance would also require depositing additional money, which could still result in excess contributions.
BMK