Two different things are being mixed together, so let me separate them.
Direct ownership: the deed reads something like "ABC Trust Company FBO Warrant IRA." The custodian signs the contract and the deed on the account's instruction. You sign a direction letter for each transaction. Rent goes to the custodian, invoices go to the custodian, and the custodian pays them. Slow, and hard to get wrong.
The LLC version: the IRA buys 100 percent of the membership interest in a new LLC, the LLC opens a bank account, and the LLC buys the house. You're often named manager so you can sign at the bank. Being manager lets you sign documents and direct money. It does not let you swing a hammer, collect rent into your own account, or use the property. The prohibited-transaction rules follow the money into the LLC, they don't stop at the custodian's door. Managing the paperwork is allowed. Providing labor or personal benefit is not, and that line is the same whether or not there's an LLC.
Why add the LLC: speed, liability separation between the property and the rest of the account, and easier joint ownership if two IRAs invest together. What you're taking on is that you become the person deciding whether each payment is compliant, with no custodian looking at it first, plus the LLC's own annual state filing fee and whatever your state charges. Some states also treat single-member LLCs differently for franchise tax, so that's a state-specific question.
Whether a manager-managed IRA LLC is appropriate for your situation is a question for a tax attorney. The structure has been litigated, and how it's documented and how you're compensated (you generally aren't) matter to the answer.
