Hey @Steven Medina
Just to share some insight from an estate planning/asset protection perspective:
I personally use a version of the structure your attorney suggested, while it is definitely adding layers of complexity, I see having all these entities as shields over your rental properties from both inside and outside liabilities. The added layers to accounting, in my opinion, is the price of admission…but as long as you have organizational systems in place then it should be straightforward accounting come year end.
RE Lenders having issues with LLCs: this is probably the biggest factor to take into account. But as you mentioned, there are exceptions that have been recognized by F/F when it’s done for asset protection/estate planning purposes. Ultimately, each lender has their own quirks regarding properties held in LLCs, and those are always fluid as well. In our experience, connecting with the right loan officer/underwriter (who understand the reasons for having properties in entities) does wonders. These entities would typically be “pass through” entities for tax purposes and thus the profits/losses would go directly onto your (and your wife’s) returns.
RE Owner Input/Draws: Yes, the most important part of proper entity structure is the "corporate maintenance" or "formalities" that must be followed so that an LLC is actually seen as a separate business from your person if looked at by a presiding Judge/Jury. This includes proper capitalization (IE if you are contributing $50 here, $100 there, to your holding LLC and then to the sub-LLCs…that won't look good). You want to make sure that every entity has sufficient capitalization to operate independently without the owners having the infuse it every few weeks.
RE Additional Tax Prep Fees: Again, being that they will likely be pass-through, these costs should be manageable. If they are not pass through, and at some point it makes sense to do an S-Corp election for the holding LLC, I'm sure if you ask CPAs niched in real estate, they would say the savings outweigh the costs. (Caveat: S-Corps are pricier for many reasons and CPAs typically recommend a certain revenue level before making that election)
RE Does it really have the protections that are worth the effort? In my opinion putting rental properties in an LLC and then having a holding LLC is like driving during the day, with your seat belt on, 5 mph under the speed limit…do you need to do all this? The short answer is no. You don't need to do any of these while driving (except the seat belt by law, although you can still choose to break it), and you can probably drive many times like this without consequence. Except for that one instance that comes along that you wish you had done of these to help mitigate the damage. I have a similar setup and we recommend similar setups because we like to have as much peace of mind as possible…even if that means a few more spreadsheets.
Sorry for the run on sentences, I think it's endemic of all legal minds :) Hope that helps.