Indeed, you can't have several values with the same "value" in the data of a custom field.
Now, there is a way to go around this.
Suppose that you need to have three values with 10% price increase. Since the custom field "values" are saved as strings the value "1.1" and the value "1.10" are not the same for it. But when the plugin will process the formula, it will result in the same percentage increase. So, you could use the value 1.1 for one, 1.10 for another and 1.100 for another. There is no limit to the number of zeros to add so, like this, you could have dozens of rows for the same price increase and it would work fine.
Regarding variants:
If you create a product X with a characteristic and you configure variants for it, you can edit each variant and use the "Main product price percentage" setting to set, for example, 110 %. If you have a price of 10€ in the main product X, the variant will automatically have a price of 11€ calculated on the fly on the frontend.
However, if you use that product X as an option of another product Y, it will still be the price of product X which will be taken into account, not the price of product Y.
It seems to me that it is what you were trying to do. But this won't work. Thus, I recommended using a custom item field with the price calculations plugin as it can do what you want.