Yes, there will be increased AC resistance just because of the high frequency AC excitation (skin and proximity effects). The PWM harmonics will also add additional losses. I am going to try to build in some features to the coil to mitigate these losses.
Have you estimated Rac/Rdc for the operating waveform? I can appreciate you may be able to modify proximity losses, but not skin effect.
If effective Rac/Rdc is more than say a few % increase, or you can't confidently model and do some form of prototype test confirmation of AC losses, then I can't see any merit in maxing out the single conductor copper area to aspire to a max slot fill %, to the detriment of a myriad of foreseen and unforeseen risks. Perhaps you've looked at other practical conductor structures and assessed that a single conductor is the best outcome for your operating current waveform.