He sold his home but picked up a couple of large Amish sheds delivered to the lake site & got permits to make it livable until he could build the new Lakehouse cottage.

Check out permitting for the additional unit to make sure it can be used as an ADU.

I have heard stories of investors having difficulty getting permits, etc.. 

As I dug further I saw that this was not the case, leading me to conclude that ultimately:My loan options are going to be limited to condo-friendly loans (probably a commercial loan on a package of properties).My ability to guarantee ongoing operations is limited (this is true in most places, but here in OKC we've seen recent examples of Owner Associations deciding that rentals are no longer permitted . . . woof!)

The area was so rural that no one needed permits or anything to do this, they just made then renovations, added letters to the mailing addresses example 123 Main St A, 123 Main St B, etc) and they were done.I am interested in buying a house with a master bedroom (which has its own bathroom) and then having a separate entrance added to that bedroom.

Know that the city of South Lake Tahoe will not allow new VHR permits except in the "tourist core" area, which is pretty small. 

If the owner simply built himself an apartment without getting the correct permit, then it was a violation of the zoning and FHA will not (or at least should not) give you a loan on the property as it stands.As @Alex Horelick said, you may be able to remove some appliances to make the kitchen not a "kitchen" according to the legal definition--that would render the unit not a "unit."

Looking to connect with an Atlanta based Architect who can help me renovate a house and who can work with the county for permits.

The owner could have done a lot of work inside the house; an easy way to find out is to call the town & ask what permits have been pulled and closed out in the last few years (building department will have this information)If my post helps, would appreciate a vote.

First thing is you never want to close on a development parcel until you get all of the approvals and permits to build what you want.That being said the best thing to do is call the city and ask them what the attitude is towards development in that area and what your chances of approval or denial look like.