As Snoopy said, power supply is very influential. Not just for Roon, true for players like MPD as well. It doesn't really make sense to me but I have since stop questioning it, accepted that and moved on.
As for what is better, Pi or Atom, it's really up to your needs, requirements and ultimately taste in music presentation. Snakeoil has that flexibility and at the end of the day it is subjective. Here are just some more objective pros vs cons:
Pi 3 - Con: Network and USB shared on the same bus. Meaning you will always have throughput (transfer speed) and contention issues (fighting the same resources)
- Con: Lack of RAM for some use cases (e.g. RAM or memory play)
- Pro: Cheap
- Con: power connector may be a weak link (may be solved if powered via GPIO).
Pi 4:- Pro: Potential for more RAM (up to 16 GB)
- Con: Dedicated bus for networking, with throughput of at least 930 Mbps or 950 Mbps
- Con: Same potential problem with power input connector (may be solved if powered via GPIO).
Atom:- Con: Old hardware with EOL support
- Con: More complex requiring more current (e.g. 12V5A for Atom vs 5V3A for Pi4)
- Pro: I'm using this as my primary rig still so have the most experience in tweaking.
So really the only advantage of an Atom board is I am still using it as my reference setup. Other than this I don't really see a point.
For now my Atom board still has the edge. Because it is using a modded UpTone JS-2, with a dedicated USB card. Vs my Pi which is using unfiltered USB port and powered off from a POE switch (SMPS).
So I guess put it in another way it depends on what you have right now, and what you intend to purchase next. If you already have USB cards (JCat/SoTM, etc) then go with Atom. If you have those USB filters, and a good LPS for Pi, go with that instead.
BTW, all platforms from 1.2.x onwards suffer from a lack of a custom real time kernel. And OS still remains untweaked. These are the two big issues I hope to solve in time.