As being part of the self-directed IRA community, I thought I'd step in and clarify this topic.
Part of the confusion is that there are not two, but instead three seperate entities involved in this type of transaction: the custodian, the beneficial owner and the IRA. The TIN being used is not that of the custodian, but instead that of the IRA trust, itself.
The custodian isn't pledging any type of collateral--the IRA is. So, if John Smith is looking to purchase 123 Main Street in his IRA, the loan is in the name of the IRA, XXXX FBO John Smith IRA XXXX, and it is non-recourse, meaning that the IRA owned property is the only collateral available.
Hope this clarifies.