I’ll add my 2 cents to this discussion. The TL;DR version is: to my ear the SP200 is the overall better amp, but not by much, with the Atom winning on midrange timbre but the SP200 being a little bit better everywhere else.
Other intro thoughts/questions: @Riya, what respective gain settings did you use? I found the Atom high gain and the SP200 “low” gain to be the most similar. This isn’t surprising givent the sources that say the SP200 doesn’t really have a true “low gain”. It’s gain settings are more like the “med” and “hi” from the 789 and 887. The differences I report below are audible on all the different gain settings I’ll describe below but are the closest when the Atom was set to “hi” and the SP200 to “low”. I think that also given what I just described, that’s the most true ‘apples-to-apples’ comparison.
Test equipment: Topping D10 DAC -> Atom -> Atom preout to SP200. Headphones used were stock HD6xx, stock HE4xx, and M1060 modded with Dekoni Elite Velour pads for Audeze and 2 ply paper towel (the Kirkland brand stuff you get in the huge packages at Costco) inserted between the driver and stock foam on the away-from-ear side - really calms the peaky-ness (but does not eliminate it) of the 1060 mids, gives them a brighter sound than stock, does reduce bass extension and quantity just a smidge from stock. Everything was connected via unbalanced cables and using SE headphone outputs.
My personal findings are pretty much in alignment with @Riya. The Atom is a little bit smoother in the mids with slightly better timbre. The tonality of vocals, acoustic guitars, piano, and common mid-rangy orchestral instruments (violins, trumpets, etc.) sound just a tad bit more natural on the Atom - across the headphones tried. Bass has more impact and tighter response with the SP200. Treble is slightly more detailed and possibly just a touch elevated on the SP200. Where I will expand upon previous comments is that I don’t think the Atom has overall ‘better’ midrange. The slightly better timbre can initially sound that way but after several midrange torture tests (check out 6:45-8:30ish of The Poet & The Pendulum by Nightwish) my ears picked up slightly more detail in the mids on the SP200. The SP200 added a slight breathiness to vocals and it resolved the reverb from instruments and vocals alike just a tad bit better. For orchestral music or harmonized vocals that are placed in various places than the soundfield, both amps imaged well but the SP200 was just a little more ‘blended’. Both amps put the intruments and vocals where they should be, but the SP200 did it a little more effortlessly and created a more seamless and continuous “blend” across the soundfield where the Atom sound slightly more, let’s call it “discreet”, meaning the individual sound sources were more individually ‘placed’ rather than just being there.
I think that if you have the Atom and don’t need the added power the SP200 gives you, I agree with previous commenters that you can just stay put. To those knocking the SP200’s build quirks - which are legitimate and a bit odd - I’ll also point out that no one buys the Atom because it’s the best built $99 amp either. Feature-wise, both have 2 inputs (the difference between the unbalanced and balanced inputs on the SP200 are basically negligible), the SP200 offers the balanced headphone jack whereas the Atom offers a pre-out.
I’ll stress again that the sonic differences I heard were very subtle. I’m able to just listen to either of these amps and get lost in the music for extended periods of time. I bought the SP200 a few months after the Atom because I wanted to try running my headphones balanced, wanted to see what the THX fuss was about, and needed more non-Schiit-y power to drive my T50RP mod. The SP200 was the cheapest entry into those things.
Thanks for reading this far. I hope these words are helpful to future shoppers considering these amps.