What you are thinking at this moment is 100% correct. In Standard AX, it’s allowed only Cash Discount for PROJECT QUOTATIONS. There is no other way to put Total Discount on header of Project Quotation.
But let me tell you some good news.
Since Project Quotation and/or Sales Quotations are using same framework and data Structure, so the fields for discounts are there, which are just hided in case of project quotation.
If you will create a Sales Quotation you will see discount fields in Price/Discount Tab.
So, as a summary these fields are there existing in SalesQuotationTable, which is used for both Sales and project quotation.
You can enable those for project with help of any developer