Okay, that works! No more flickering graphics issues. However!!!! At first I made a patch PKG to simply change the config file via SLUS-21104_cli.conf, but it didn't work. I got concerned because TWO fixes from you not working? Blegh, didn't believe it. So I uninstalled the game and completely remade the entire thing, this time incorporating the clut-merge hack into the base config.txt, and it worked fine.
I'm going to go back and retry AC Zero now, this time without patching the fix but adding it directly to the game's primary PKG. I wonder if that'll work?
~edit~
Okay, still no-go on AC Zero. I even tried using the new emulator from KoF98UM, but as soon as the PS2 logo disappears the PS4 throws a strange error and states my user will be logged out due to an error, forcing me to log back in again. So.. yeah.. weird.
~edit~
Testing more games now.
God Hand seems to run fine but has quite a lot of geometry errors randomly.
SNK vs Capcom Chaos doesn't like 2x2 uprendering, causes sprite corruption, but also has no on-screen display at all -- no health bars, super bars, timer, etc. -- with or without 2x2.
~edit~
Never mind, I used the clut-merge hack and it fixed the UI/hud issues in SvC Chaos and, surprisingly, if you leave the "Screen/Graphics" mode on "Normal/Type A" then there's no sprite distortion or lines/boxes issues, even with 2x2 uprendering. Nice. I wouldn't have ever thought to use this if it hadn't been for the PSU flickering issue, so thanks again
@kozarovv!
~edit~
Hahaha, wow. Looks like Samurai Shodown VI is *actually* Samurai Shodown Anthology, they've just got a LUA file setup that not only adds a new video menu with various overlay modes (like 480p with scanlines) but it's also set to skip loading Anthology and go straight to loading SamSho6 from an ELF on the disc, then to remove the "Exit to Main Menu" option from SamSho6 so that nobody ever really knows that it's Anthology.
WEEEEEEEEEEEEEEEIRD. Why go to all that trouble? Why not just... yanno... release Anthology? Even the config and trophy files specifically state "Samurai Shodown Anthology", but the trophies themselves are only setup to function and unlock in SamSho6.
Anyway, I think I've been able to grasp enough of the config file to comment out/remove their calls to hide menu options and boot straight to SamSho6 ... so hey, let's see shall we?
~edit~
I DID IT! Holy shit, I really did it. I was able to remove the "boot straight to SamSho6 > hide exit game menu" rubbish they put in, whilst still retaining the speed boost/etc from their fixes. Basically, SamSho Anthology is now 100%. No graphics errors, no slow down. Man this feels good

Can even retain the new menu they put in for SamSho6, which lets you run with scanlines and bezels too. Sadly I'm not entirely sure how to make that function for the rest of the anthology, only 6 since it has its own separate ELF which the LUA patches.
Still, it's perfectly functional *and* it means SamSho6 gets the added features from the PS2 Classic official.