Estimates are NON posting, you could put a charge of  million bucks on an estimate and it is impossible for it to affect COGS or anything else. Estimates include what you propose to charge a customer, not what you actually charge. Your Products/Services can have both a selling price and your cost, and the markup is built into the selling price. 

If your going rate to perform a service is $100/hr you just enter the hours. If you sell widgets that cost you 99 cents for $5 Your estimate is going to say $5, unless you override it.

Markup from your list price is as I see it only necessary when you are buying something you do not normally sell and wish to add a markup.  You always can do this with billable expenses from a bill or expense to an invoice.

Estimates serve no income purpose until they are converted to a sales receipt or invoice. If you have used billable expenses then you can add them to the invoice you create from the estimate replacing your estimated charges.