We don’t have any kind of designation on the deed, but......that seems it is just a “description” made in the deed by the seller and buyer, and would have no affect on the legality or permitted use.

As a point of comparison, I spoke with an architect as well, and his all-in estimate of design plus construction was not too far off of the design/build quotes.The kitchen would be brand new (it doesn't currently exist). 

I am not a Structural Engineer, Achitect or any other kind of Design Profesional. 

But the most accurate way to get an idea of design is to see what is being done in the areas in which you plan to flip.

I feel a lot of design details can be taken from this industry.

We build the cost of design into the budget.  

Every piece of automated equipment is conceptualized by marketers, developed by a myriad of designers and engineers, assembled by workers and production support staff in factories, who source components from countless companies employing their own workers and raw materials sourced by purchasing and logistics.  

Aside from the above, you must learn your market first, learn how to estimate rehab costs (as a contractor, that should be easy for you, but having knowledge of design and what items bring the most resale value are also needed) and how to estimate the exit values.

Would you recommend a certain architecture/design software for people who do not have a lot of design experience and really just need it for more basic building permit proposals?

Use what you learned in the book and look at properties for sale and go through the pictures and do your own estimates until you get a general sense of how much a rehab costs based on the your level of design and the home's level of disrepair.