We have similar problem here..
It’s not about the theme.
It is also happen when the products is out of stock.
When you UNREQUIRE the custom options, the checkbox will show.
However it is still useless. Although you have checked those related products, they will not be added in cart when you add a product to cart along with them.
Your products’ option still need to be selected, otherwise it will raise an error (No SKU) when you add it to cart.
It seem the custom options don’t have default value too. Should it have, it would be better.
Then the question: how should we treat this behavior? how to make it more user friendly to our customers?
Some guys added explanatory statement inside the related products. But in our case we have a lot of products who have the custom options.
Any help or suggestions are really appreciated.