It’s all the same, really; there will be no perceivable difference between an RGB signal with composite or separate horizontal/vertical sync, because it’s all still RGB.
Where you may see a quality difference is in the cable you use. If you buy crappy cabling, you run the risk of visual noise and audio hum, which can be more noticeable with SCART, due to it carrying both audio and video in the same cable; however, these problems don’t really occur with good, shielded cabling, and shouldn’t occur at all with the pro coax cabling you can get from Retro-Access or the Packapunch cabling from RetroGamingCables.
Personally, I prefer to have my Toro box connected to my OSSC via SCART, because it gives me the convenience of one cable for both audio and video, as well as not having to reconfigure AV3 for the correct aspect ratio (Dreamcast requires 480p DTV for a 720×640 frame size, but AV3 defaults to a 640×480 frame size).
If you decide to go with SCART and you’re in the US, I recommend getting one of these KabelDirect SCART cables to start with; they’re very cheap (Currently $6.39 US for the 10ft and 15ft cables; 6ft is double that), very stiff, and decently shielded. I haven’t spent much time with them, but I did confirm I no longer get the nasty audio hum I was getting with the $6 basic SCART cable I ordered from BeharBros with my Toro.
As far as 480p compatibility, you can trick some games into using 480p by flipping the far-right switch on the Toro so the console starts in 480i mode, then flipping the switch back to 480p when you see the white Sega licensing/Windows CE boot screen. This works perfectly for me with Bust-A-Move 4. For games that simply aren’t compatible, you might be able to find a patch online, or you’ll have to deal with your TV’s deinterlacing, or the OSSC’s bob deinterlacing.