If you have to reconfigure an existing building, you would have to budget for removing demising walls, altering utility connections (plumbing & electric), HVAC, and/or moving tenants to get you that contiguous big space. 

But yes, for most people it's completely unnecessary because 1) Single member LLCs can be pierced if they are used like an alter ego and 2) if you buy with a mortgage the bank will make you sign a personal guarantee for the LLC, which is just like not having an LLC at all, except with additional fees attached. 

I would recommend looking at the "Alteration Permit" section to see the GC, as the other permits were probably pulled by his subs 

Absolutely never ever alter your investor’s interest in the deal, even if you’ve returned ALL of their capital they still get the percentage of distributions that they were entitled to day one.

While these goliaths have certainly made their presence known by gobbling up huge chunks of market share, and permanently altering the appraisal profession’s model along the way, I am happy to report there are still local and regional appraisal firms surviving.

Any HUD purchase I've done it specifically says it is not assignable and that the contract is void if altered in any way.

My experience is if you have an (A) plus site meaning almost the best in town and not a B to C site then sometimes STNL tenants will alter their layouts to try and make the site work.

When you talk to town planning, ask for a list of surveyors and trades people (specifically well and septic at the Environmental Health Department) since you'll need these permits even if there is an existing well and septic since you are technically performing an alteration.

Lease clearly states no alterations. 3.

The suggestions you have been offered can dramatically alter the trajectory you are on in a positive way.Cheers to your success so far!