I will spec materials/colors/repair method when I feel it needs to be done a certain way or I want something different/special.  

What are the industry standard marketing and design tools people use to create marketing materials and OMs for commercial real estate?

Add into the equation the cost of materials and it makes sense that builders are finding ways to cut overall build costs and one of those ways is to buy land cheaper. 

Here's some basic beginner advice with some reading material that will answer 80% of your questions.1.

From my experience (I could be wrong) there isn't a format but the estimate should list details like the materials to be ordered and the hours of labor needed for each repair project (for example the kitchen cabinet installation or exterior doors) along with a cost listed for each line item.

The handyman gave me a quote for $5000 and $300 for materials.

You need a good lease agreement, landlord forms library, educational material, and landlord attorney to guide you. 

The quote was $5352.00 ($3,650 for labor and $1,702 for materials).

Contractors don't make a living off marking up material prices.

What if the new owner backs out of the job and gives it to their "regular guy", will the original contractor come after me for any expenses/materials spent?