Hi,
The options will automatically take the warehouse of the product when the "group options with product" setting of the HikaShop configuration is activated.
That's because when the options are grouped with their product, they appear as one product on the cart and the shipping methods selection interface and thus are bundled together with their product in the shipping method selection per warehouse.
If you turn off that option, options won't be associated with the product and they will be keep their own warehouse for the shipping method selection.
Regarding the restrictions per min/max quantities, the weight of the products are not taken into account. What matters there are the number of products/options regardless of their weight.
If you want to not count the options then don't use the quantity restrictions, use the weight restrictions instead:
set a weight of 1kg to all the products and a weight of 0 to the options and then use the min/max on weight. That way, you'll get the same calculations but without the options taken into account.