ATmega ADC input channel analog vs digital power
If the device specifies it uses DVCC (Digital) for a channel, that would mean that its initial stages are powered by the noisy digital power. So some noise may/will couple into your signals there, even more so if your signals are particularly weak/high-impedance.

Coupling the DVCC and AVCC through an LC network is exactly the right way to keep the Digital noise out of AVCC, so yes, it could still matter. The inductance the datasheet advises keeps high frequency switching noise out of AVCC and the capacitor helps that along, by shorting away those noisy peaks and also storing some "spare" power for the AVCC domain.

So, if you filter your AVCC domain with an LC network and then use the DVCC powered channels, the first thing you should check is if those signals are relatively strong. This will avoid a lot of the noise, since the ADC presumably still works on AVCC. And then try to avoid them fro signals that then would still be sensitive to 1 or 2 LSB of digital noise.

That is, if digital noise matters at all to you, there are some possible applications that would not care about digital noise all that much, but that's down to you, I suppose. It might even be awesome to have a little digital noise for free, if you want to use oversampling and decimation, but that's a WHOLE other chapter.