Better is a subjective thing. There are things that can be done but it depends on what amount of effort and how much charging the iPod is worth to you.
I mentioned previously, a way to check whether it is a ground loop by connecting just the ground of the connector, or whether it is the buck regulator noise getting back into the system from the USB charger circuit, combined with the obviously low PSRR (power supply ripple rejection) of the new stereo.
For example, if your ipod goes into a low power mode where it doesn't power the screen, or maybe even if it does, the question is how much current it needs to stay level on battery, so at least it doesn't discharge even if it doesn't charge. The direction I'm going here is that you then wouldn't even need a switching buck supply for USB 5V, could just do it with a linear regulator which produces practically 0 noise, "if" it's the switching circuit causing noise instead of a ground loop.
If it's the switch circuit, a simple textbook LM7805 regulator circuit could supply power to maintain the same charge level, or a different 5V output buck switching PSU module.
If your current USB charger has a casing that allows opening it, it could even be as simple as switching the input capacitor to shift the noise frequency or magnitude.
The ease in doing any of this, depends on too many factors to consider remotely. I mean there's even the option of just sending the radio back if it can't reject the noise, get a refund and start over there, or just have a portable USB power bank that you charge every once in a while, to power the ipad, or what I already suggested, that you shouldn't really need 100GB of music as that is more than you could listen to on the longest of trips.
Suppose very high bitrate MP3, arguable an inaudible difference between it and lossless FLAC. That would make the average song about what? Just throwing a # out, lets say 10MB per song. With a 32GB limit (if there really is one, see my prior post), that is still over 3000 songs, and if you're on THAT long a trip, can't you just take a 2nd 32GB flash drive with you and swap it during the days to weeks it'd take to make it through that many songs?
It seems like you want to make it hard on yourself and I am willing to help you do that, lol.
The easy answer here is that if you want more than 32GB support, you get a stereo head unit with more than 32GB support. Tethering a host phone or tablet to do this then run a charger and cable too, is a fiddly hassle compared to the stereo head unit doing it all itself.