What are the most common challenges investors face when securing fix and flip loans, and how do they overcome them?

Piercing the veil is very common. 

Examples of common objections include needing to discuss with a spouse, feeling it's not the right time, uncertainty about the location, or having funds tied up in other investments like a 401K, 1031 exchange, or the stock market.

I utilize professional Autocad software.

However, if have several rentals and need to deposit checks, or use a debit card to pay utilities and other bills, etc. conventional business bank account would be the best choice. 

While the bookkeeping will likely be complicated, is the accounting/taxation on this STR based on 100% STR income/expenses allocated 100% to business and general house expenses (mortgage, utilities, depreciation etc) pro rated between STR/personal residence based on sq footage?  

And if they are, and you have not sold your property interest, explore common strategies like 1031 exchanges.

It's a commonly applied local overlay in the 'usual suspects' of States that have restrictive tenant protections, so its unfortunate that you thought you didn't have to accept it...technically you may not have been required to 'accept the voucher', but you have to allow them the opportunity to apply and then allow the housing office to decline the property. 

Quote from @Shane Bishop: Software is a common question on BiggerPockets.

Fairly common.