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.

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

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

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

One thing for sure; thanks to the new tax plan accelerated depreciation is about to get materially even better!

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

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?

That property was run down, smelled funny, and it looked like the cheapest materials were used in there which are just going to fall apart year after year. 

The material is interesting, there is no upsell, and you do get a fancy certificate by email.

Are they simply home improvement material hobbyists because they left money on the table?