Is there a way to make a custom field to display the MarkUp and Margin of an item in a inventory report?
As far as I'm aware, any Retail custom fields are primarily accessible via the API. Not on canned Retail web client reports or Analytics reports. The only exception is custom product fields are visible and accessible in the product detail form in the web client.
If you are looking to see these two calculated product fields that are displayed in the product detail form, perhaps you could export a canned Retail web client report to Excel and run calculations there. Or Analytics allows you to create your own calculation columns if I'm not mistaken.
Did you see in Reports>Inventory Reports>Assets
That report has a Margin column, alas not the Markup one but both can also be calculated based on your Retail and Cost values.