A little bit of history...
The current version of Atom FPGA was started by Alan Daly in 2009. It used an Olimex Mod VGA board:
https://www.olimex.com/Products/Modules ... e-hardware
The Olimex board was designed as an open source implementation of the GameDuino FPGA-based graphics card. It uses a standard VGA connector, and allows 3-bits of Red, Green and Blue (so 9 bits in total).
Because of this, Alan's design used three bit colours.
https://github.com/hoglet67/AtomFpga/bl ... ic_top.vhd
The current AtomFpga_Core is a direct descendent of this, and has carried forward the idea of using 3-bit colour values internally:
https://github.com/hoglet67/AtomFpga/bl ... a_Core.vhd
Each FPGA Board wrapper then maps these 3-bit colour values to whatever the FPGA Board actually supports.
So I would say the idea of an Atom with multi-bit RGB at least dates back to Alan's work.
In fact, it likely goes back even further than this.
The earliest Atom FPGA implementation I'm aware of was created by Keith Howell, who is no longer active in the retro scene (as far as I'm aware). He called this "the PolyMorph" because the same hardware could imlement several machines.
His Atom design was never published, but it did exist, and it's well documented here:
http://members.casema.nl/hhaydn/howel/l ... roject.htm
This actually had a programmable palette (in the FPGA) and used three TDA8702 8-bit video DACs.
Keith did this in ~2003
Archive.org has some captures of his original website:
https://web.archive.org/web/*/http://ww ... roject.htm
So the earliest mention of a Atom with a programmable palette is Feb 3rd 2004.
Edit: Or is it....
Here's an article from 1994 written by Roland:
http://www.acornatom.nl/atom_nieuws/199 ... 942035.htm
As far as I can see, this this is giving an Atom (in PC) a palette with 2-bit RGB (64 colour) using PC's the EGA/VGA card.