Seems like a goofy deal footnote that is a disadvantage for you.

I've found some info here and there in podcasts and a little in a book or two but I'm looking more for a workbook maybe on how to evaluate them, set them up, find balance and weigh advantages and disadvantages. 

Select from a larger selection of properties for sale (in any condition), including condos, townhouses, mixed-us, multi-family, single-family dwellings and those that do not currently meet FHA standardsWhen offer is presented properly to seller, 203k offers may be advantageous in a competing offer situation as the seller does not have to fix-up or repair the property but instead allow the buyer to include these items into their 203k mortgage and complete the improvements after closing using the buyer's own style and design.203k Benefits to Home Owners & Sellers (not all inclusive)Market property to more buyersAllow buyers the opportunity to renovate, upgrade or improve to suit their tastes and preferencesNo need to settle for low-ball cash offersCurrent condition of property not required to meet FHA's property standardsBuyer is permitted to correct any property deficiencies after close of escrowNo more inspection concernsAbsolutely no repairs are required prior to close of escrowSeller not responsible for cost of repairs/improvementsTransaction will close with property in "AS-IS conditionClosing occurs in 45 days203k Benefits to Realtors® & Lenders (not all inclusive)Increase income by selling more homes and originating more loansRaise real estate values by improving homes and neighborhoodsDecrease foreclosure inventoryHelp buyers who previously could not buy homesHelp seller/owners with properties in outdated or fix-up conditionSpur economic growth by creating job opportunities for the construction/remodeling industryPromote an under-utilized niche program that not many Realtors® or Lenders understandRevitalize your community203k Disadvantages (not all inclusive) upfont MIPMI for life of loanSupplemental origination feeInspection feesTitle update feesmore complexmore moving partshigher interest ratepossible longer closing timeBut working with the right 203k Lender, a contractor with education/experience with the 203k, such as a Certified 203k Contractor, the benefits can definitely outweigh the disadvantages. 

One disadvantage all of them share is that you put in numbers (ARV, purchase price, rehab, taxes, etc.) and get either MOA (max allowable offer) or profit/cash-flow numbers. 

What other advantages or disadvantages to going either route have you found?

Also you need to evaluate how much of your own cash you are willing to play with. like @Jason Hirko said, if you get a AA property, its highly likely there is no value to add which puts you at more of a disadvantage to getting the most out of the property.

Having cash can be a disadvantage actually

The disadvantage of setting up entities is the the extra paperwork it generates with filing at the state level and filing taxes.

Can someone explain to me the different advantages and disadvantages of working at a brokerage with a percentage based commission vs flat fee?

Some students apply the principles to smaller properties, but there are disadvantages to working at a smaller scale, so it’s not too common.