Short Q&A (thanks to danboid from uzebox.org forum):

Q: Can I sacrifice any Atari ST to build an Atari ATX or can only specific models be used?
A: You can use any Atari ST - German, UK or US - it doesn't matter, but I've tested it only witch european PAL chips.

Q: Can I get video out of an Atari ATX without having to buy a VGA card?
A: Yes, there is standard DIN13 video output on rear panel.

Q: How many people have built one apart from you?
A: I don't know, but I think there should be about 10-30 boards.
Also there is a guy, who made some mods:
https://chillichai.com/atari-st-micro-atx/

Q: Can you estimate how much the BOM would cost after I've bought a suitable ST to sacrifice for it?
A: It's hard to estimate. Except buying Atari ST for chips, You also should have some IC sockets, pinheaders, TTL chips, rear panel sockets, resistors, capacitors, transistors. 
Small parts You have to buy in 100pcs packages so it will increase cost. Hard to say but it should be about 50$. Also You have to buy 39SF040 and PIC16F876 - they are available only from Aliexpress.

Q: Can it play all Atari ST games without issue?
A: I think it should because board is 100% compatible with Atari ST, but I've tested a few games and demos only.
But remember: there is no Blitter and there is no cartridge slot.

Q: Any other gotchas or issues I should know about? Are any of the BOM components hard to find or expensive?
A: Like I said: PIC16F876 is hard to find in official sources.
Also 5V generators: PAL 32.084988 MHz or NTSC 32.04245 MHz are really hard to get. You can desolder them from Atri ST or most probably You will need to build them using crystal oscillator and HCU04 (U - unbuffered) TTL chip.
Oh, and memory module - You have to desolder old SIMM memory module to get chips. In those days there were EDO and FPM chips and unfortunetely the most popular type is not compatible - only chips with "0" at the end of symbol works fine.
Also WD1772 is very expensive and/or hard to get, but if You'll sacrifise Atari ST - problem solved :)

Q: Is it good project for beginner?
A: No, definitely no. There is a lot of small SMD components on bottom side.