Stratix II: Coil circuit

It's not clear to me, in which regard transmitted power is relevant for your application. Although the coil is a reactive load, part of the power feed is consumed by losses, a part is transmitted to the secondary and a small part is radiated. The general limits for radiated emissions correspond to a few µW RF, to give you an idea of the order of magnitude.

As you mentioned above, you connected the coild to a digital pin through a series resistor. I don't see, how the FPGA should filter the signal, it's a squarewave anyway. So only an external filter seems to be possible.

I previously mentioned, that a filter would be necessary if you utilize an ISM frequency. Otherwise, your circuit won't comply to EMC regulations anyway, at least if the coil has some extension related to the wavelength and the transmission path isn't shielded. There are additional rules, also some national regulations, that define, which frequencies and how much transmitted power are allowed for particular RF applications.