They are working on a replacement motherboards, but you have to have a few chips to insert.

An issue is that many chips are not documented, making it hard for FPGA programmers for example.

Lots of custom chips especially on Amiga, also for C64 (SID, VIC-II).
Since you can't source those chips expect by getting them from old machines there is not much point. Of course you could remake this chips through FPGA (there is a solution for SID, don't remember the exact technology), but then you could as well put everything into one FPGA if it fits.
Those other homemade machines only use off-the-shelf components. Should be enough to run CP/M with a Z80.

I'm wondering, is the documentation about these custom chips lost, or are the right holders protecting them / not releasing them?

Paula, Gaile, Denise and some other chips, can be found on eBay.
I checked really quickly last night, on my phone-app, and they are in the pricerange of aprox. 15 US Dollar's a piece.
I bet some of the ram-chips can be found too. They are just second hand, most of them.

We might get them next year: http://wiki.icomp.de/wiki/Amiga_reloaded

I've been hearing rumors of an Amiga remake for years. The community is crazy. I've yet to see anything out of them that wasn't either a super expensive board that at the end of the day used UAE to bridge the gap or ended up vaporware.