Is it permissible for the seller to keep a percentage of the sale price set by the shop owner, especially since the shop owner did not explicitly state that?

If the owner gives his worker a garment to sell and tells him: "Sell it for such and such, and whatever exceeds this amount is yours," then the contract is valid. However, if there is no custom or common practice for this, then the excess belongs to the owner of the shop, and the worker is entitled to a fair wage (ajr al-mithl). It must be noted that the recognized custom is that which governs the method of determining workers' wages, and not what workers agree upon among themselves without the knowledge of the employer.