Boss bonus only work on non-unique items.
This phrase is somewhat vague, and we are not sure about which items it does really affect when talking about rare from bosses.
We know, for sure, it doesn't work on Ferumbras' hat, for example, but we also know that it is a guaranteed drop, so it is easy to prove it does not double it.
As far as what I've been able to see from my boss hunting and boosting, it does not work for the rare itens on bosses. So you are most likely wasting money by boosting it. Regardless of that, I cannot be proven unless someone has a printscreen of 2x amulets from the Welter or 2x Glass of Goo from Shlorg. So far, I haven't, and all screenshots with double loots has been of two different items in the same boss, which is totally possible without boosting it.