GST paid to the govt is based of final selling price, the price that is printed on the invoice.
So by adding 6% in earlier, the calculations will end up the same.
No flaws there.
no la, say if item costs RM5000.
scenario A - GST paid = RM600. Profit = 9010 - 600 - 5000 = RM3410.
scenario B - GST paid = RM510. Profit = 9010 - 510 - 5000 = RM3500.
any corrections are welcomed, cos this is how i see it 
Both scenarios the shop will pay rm510 in GST as the GST is calculated on the final price paid.
The figure that is printed on the invoice.
The one that will be paying the GST is the consumer alone.
No matter how much the item costs and how much is the retail of the item with GST included... After discount, u pay the price and the GST will be the same amount in tandem with the discount.
It's a consumption based tax so the one ultimately footing the bill is the consumer.
An item that has a retail of rm10,600 (assuming with GST included) does not mean the shop has already paid govt the rm600.
As long as the item is left unsold, the price tag is just a figure printed on a tag. (at this point, only the GST of 6% based on cost price is paid to the Govt)
Once the item is sold, then the shop will have to enter the amount into the POS system then the shop will need to pay the GST to the govt... Whereby the money comes from u anyway.
I will use your scenario as an example with the "cost of the item" being rm5,000
Shop purchases stock from supplier.
GST paid to supplier rm300 (based on cost of rm5,000)
Item now placed on display with a rrp of rm10,600 (with 6% added in)
Item not sold, GST of rm600 will NOT be paid to the Govt.
But the Govt have already received the 1st tier of the tax which is the rm300 paid from the shop to the supplier and the supplier to the Govt (assuming no more chain of supply on top on the supplier)
If the item is then sold at retail price. The CONSUMER would have paid rm10,600...
Invoice will then list the price as rm10,600
Shop will now enter the amount into the POS system and they will compute as rm10,000 + rm600 GST.
Shop will now pay Govt rm300 as the earlier rm300 is to reimburse the rm300 that the shop paid to the supplier.
Now assuming item is sold at a discount. 15%? ok
Invoice will now list the price as rm9,010
Shop will now enter the amount into the POS system and they will compute as rm8,500 + rm510 GST.
Shop will now pay the Govt rm210 as the earlier rm300 is to reimburse the rm300 that the shop paid to the supplier.
Now assuming price listed is not GST inclusive.
Shop listed at rm10,000 and sold it at a 15% discount.
Invoice will list as rm9,010 (10,000 - 15% + 6% GST = rm9,010)
In both cases, the shop makes exactly how much it's suppose to make without the GST eating into it's profits.
