It’s true that the free online calculators do not take the datalink protocol into account. The datalink protocol could be PPP or ATM etc. and would add to the overall badwidth requirement.
But, the protocols you mention are not layer 2. IP is a layer 3 protocol (network). UDP is a layer 4 protocol (transport) and RTP is a layer 5 protocol (session). These three protocols are taken into account by the calculators.
For more information about the layered approach, you can study a document we published online.
Downloadable versions which also take layer 2 into account are available for purchase.