The Manual Line Discounts are applied after all the System Discounts including THRESHOLD discounts, hence it results in final discount amount difference in MPOS.

Scenario:
Threshold Discount - $10 OFF $100 Purchase
Manual Line Discount - 50% Off [Clearance stock]

Current Shopping cart:
ITEM NAME PRICE QTY AMOUNT

ITEM001 ESTEE LAUDER NGT SOL 100.00 1 45.00
$10 OFF $100: Discount 10.00 (10.00%)
Line Discount: 45.00 (50.00%)

Expected:
ITEM NAME PRICE QTY AMOUNT

ITEM001 ESTEE LAUDER NGT SOL 100.00 1 50.00
Line Discount: 50.00 (50.00%)

* When line discount is applied, the Threshold discount condition for $100 is no longer valid, so it should not be applied.

D365 shopping cart evaluates all the System discounts[Simple, M&M, Qty, Threshold] based on priority and this includes the computation of Threshold discounts after all the other System discounts[Simple, M&M, Qty] are applied.
If the Cashier applies additional Manual line discounts(e.g. Old Stock , Display Set, etc) then this LINE Discount is applied after the THRESHOLD Discounts which is against the retailers expectations.

This feedback is to ensure that MANUAL LINE DISCOUNTS is applied on the line as lowest priority while all the other System discounts(if applicable) are applied. Then THRESHOLD DISCOUNTS evaluates the cart in entirety and applies after all the line discounts(System + Manual) are applied.
This is much needed functionality for the Retailers.

P.S. Workarounds like Split Receipts, Price override, new item creation for Old stock clearance , etc are not feasible solution for Retailers as it affects the Cashier operations or company policy limitations.