Hi,
I've done some tests on my end and the plugin works fine regardless if the products have variants, options etc.
When you have variants, you need to set the deposit percentage in the custom field in the settings of each variant (that way, you can have different deposits for different variants of the product).
So if it doesn't work on your end, it's either that the custom field is not configured properly, or the plugin is not enabled, or the deposit percentage value it not entered in the custom field of your products/variants.