There's a full clone of a revision 0 Apple II motherboard made by one avid retrocomputing enthusiast.
He no longer has kits for sale, but the board Gerber files are available. Order some boards from a PCB manufacturer, source the components, and you'll have everything to build your own complete Apple II mainboard.
I have a strange desire to make an imaginary competitor to the Atari
So there are a couple of places one could build a better 800 and still be entirely within the 1979 (well actually, 1978) tech tree. There's also some things that might not have been possible. So here goes...
The Atari was odd (unique?) in that it did not interleave memory access ...
I would simply consider the complexity of the ANTIC, POKEY, and GTIA chips -- how many transistors etc., and use that as a transistor budget for your gate arrays.
Simply assume that the designers made the chips "as complex as they could given technology and economics", and use them as a benchmark.
Also, you need to keep the clock rates down like they were ...
The MiSTer project is an Open Source effort to create clone consoles/computers on the Terasic DE10-nano FPGA dev kit
They have an Apple II+ core available and the MiSTer can be configured to boot directly into it
I have a very similar desire as you. However, mine goes much deeper. I have a desire to create a competitor for the following: KIM-1, Atari 800, NES, Apple II, etc.
In 2018, I created, designed and produced my first SBC that could have been built in 1979 and would have competed with the Apple II.
So I have a little bit of experience but I'm no expert.