Idk why the Dreamcast appreciation and emulation thread is locked so I'll post here.
It took me too damn long to realize this. Using RetroArch and Flycast (to me the best Dreamcast emulator by far) and keeping what I thought was system accurate options for the most part, The King of Fighters: Dream Match 1999 of all games kept having these weird seams on the sprites indicating some kind of upscaling at work. I "knew" I wasn't upscaling since I left the default 640x480 so I couldn't explain it and chalked it up to bad emulation for that one game. After pondering it today I realized this is one of the games that actually used the Dreamcast's 320x240 low resolution mode (that a Dreamcast switches to after the boot up screen but the emulator forces everything at the preset resolution), those that didn't support the VGA cable and couldn't even be forced to do so. So yeah, you're meant to emulate this game in 320x240 folks, then it has no graphical issues (on Flycast, though the boot up will look all pixelated).
For future reference (though maybe not all present issues, some are fine with getting upscaled) google says these are all the 320x240 Dreamcast games:
Bangai-O
Black Matrix
Gunbird 2
JoJo's Bizarre Adventure
Marvel vs Capcom
Princess Maker Collection
Street Fighter III: Double Impact
Street Fighter Alpha 3
The King of Fighters: Dream Match 1999
The Last Blade 2
Twinkle Star Sprites
All (?) other games that look like they should be low res like these, such as Giga Wing, The King of Fighters 2k1/2k2, SSFIIX, etc., are upscaled by DC internally to 640x480.
As a bonus by holding Start + L as Street Fighter III: Third Strike boots up you can also get the proper crisp pixel non interlaced/non upscaled 320x240 output mode on that.
Funnily enough that one first showed me Dreamcast 2D games often looked ugly due to the internal upscaling causing thinner scanlines every half row of art pixels (every row of output pixels) so I opted to play/emulate the arcade versions instead (except for exclusive editions like the above KoF) yet it's the one game you can fix.