Razoola (./63) :
Sounds like we have similar backgrounds. I programmed C64 and Amiga also but have long since forgotten the hardware specs for both. I don't have any real x86 experience but I do also use Easy68k

Nice! Today I heard a funny analogy from a colleague to explain this effect - although for a 1 year timeframe already, regarding his dissertation . He said, that he has kind of a ring buffer in his head, where everything gets overwritten quickly by any new data and experiences.

One of my long term friends is currently working on a selfmade GPU for Amiga. There are interesting options nowadays (Mega 65, FPGA based emulator platform, etc.).

NeoHomeBrew (./67) :
Maybe you could "turn off" the screen by writing solid black fix layer tiles on the screen (for one frame) to hide the sprite layer while you are updating the palettes?
Possibly the snow effect could be hidden with fix layer tiles too?

Or if your render method is fast enough you could maybe increase the resolution by displaying only the half of the screen lines per frame
(similar to interlaced video: https://de.wikipedia.org/wiki/Zeilensprungverfahren) but it could cause the screen flicker too much.

Interlace should work. Available rendering time will be reduced, while amount of pixels to be rendered goes up. But this will always be a tradeoff between effect computation done and screen size and resolution.
Blastar already tried switching off the fix layer following one of my suggestions (see first page). Only switching off the display via REG_ENVIDEO worked:

blastar (./23) :
on real hardware:

move.b #1,REG_DISBLSPR
move.b #1,REG_DISBLFIX
=> black screen with random pixels

move.b #0,REG_ENVIDEO
=> black screen without random pixels