Almost every core runs about the same in between HOS and Lakka.In the case I don't want to mix nsp backups and retroarch in the same sd, I assume I just need another SD card and plain install Atmosphere and Retroarch or put Lakka in it and launch from Hekate. Is there any difference between these two methods? Do Retroarch via ATM and Lakka both run at the same performance?
The only notable exceptions are perhaps Dolphin, and other 3D cores that don't have a HOS/Switch target yet, or in other words, cores not available in HOS compared to Lakka.
But as far as shared cores between the two, they're pretty much interchangeable.