Don’t you just want to pull from the item costs that already exist for your stock/non-stock items rather than enter in new data?

If so, I believe there are multiple ways to achieve this. The easiest may be adding a side panel to that screen. I’ve attached a GI that could be used as a side panel on the SO screen that achieves a rough profit assessment - you can copy the concept over to the quote screen and edit to include a freight estimate if you have that available.

We calculate the profit/margin (with freight included) for every order once the order is complete, but here I have just added a new side panel to the SO screen which provides a pre-freight margin.

In this case, the items quoted are never consistent - we make windows and doors - the lines on the quote would be for example, "house lot of 15 windows, mixed sizes". Due to this we need to enter the cost that we expect so that GP reporting could be achieved. At present we use project quotes, but I'd like to use sales quotes if possible 

Understood. It sounds like you need to add a couple new fields to that screen.

1. An entry field in the line details where you enter the expected costs
2. A calculated field in the header that calculates the margin based on the data entered in the details.

Your VAR should be able to help you with that customization.