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This is a no-braining download, thanks
Ha, I was just struggling with this, this week. Turned out I had to delete volumes with diskpart (on windows10). Finally got to put chd's on cart for g-net multi using the 'g-net flasher' tool.
I decided to try this out but I'm having problems right on the first step.

I first tried cvs2 which uses gdl-007a.chd, just like the example.

I typed:
chdman.exe extractcd -i gdl-0007a.chd -o 1.cue -ob 1.bin
and I got this response:

chdman - MAME Compressed Hunks of Data (CHD) manager 0.152 (Dec 24 2013)
toc->numtrks = 0?!
Unable to recognize CHD file as a CD
I'm using chdman from mame 0.151 just as the example suggested. I believe my CHD files are from mame 0.156

I tried a few other NAOMI CHDs and I get the same response from all of them.
That's the problem, the version of the chd and chdman.exe that you are using. They must match.

It's not like mame changes it in every new version, but between 0.151 and 0.156 there is obviously a change.
I didn't realize that they needed to match.

I grabbed MAME .185 and matching CHDs (since that seems to be the latest CHDs on Archive.org) and got them extracted!

I used ISO buster to extract Track 3 as RAW without problem.

Then GDROM explorer gives me this message:

Unable to retrieve the bootstrap from the image file track03.bin
I tried both GDROM Explorer 1.5.0 as suggested in the guide as well as the newer version 1.6.3 (which I think is the newest?) even tried extracting again from ISO Buster and starting again from the CHD with a different game and the result was the same.
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off the top of my head that bin file could already be the bin file that you can transfer to the naomi. You will need to decrypt it thoug, using the DES key for that game.
if track03.bin from ISO buster can be used as-is then why do you have Step 3 in your guide? Also how would I decrypt with GDROM Explorer if GDROM Explorer wont open the file?
it's an ISO, you should be able to open even with WinRAR and see the content. Try opening it with any ISO editing program like IsuBuster
I tried this:

on step 1 instead of
chdman.exe extractcd -i gdl-0007a.chd -o 1.cue -ob 1.bin
I did this:
chdman.exe extractcd -i gdl-0007a.chd -o gdrom.gdi
I then skipped step 2 and opened the .gdi file in GDROM Explorer... from there I was able to view the data track and decrypt with the DES key and extract it to a bin. I ran out of time so I haven't tried writing the file to CF card yet but I'll report back once I do.
I had the same experience as @twistedsymphony when working with Outrun 2 SP Japan Edition.

I simply used:
chdman.exe extractcd -i gdx-0011a.chd -o gdrom.gdi
My CHDMan tool came from the latest Mame release .exe's mame0201b_32bit.exe

Next I went to CityLan and got the DES key...


From there I used GDI Explorer 1.5.1 (jc-gdrom-explorer-v1.5.1.zip), as version 1.6.2 crashes on my Windows 10 instance (jc-gdrom-explorer-v1.6.2.zip)
Go to Tools, choose "Decrypt a Naomi binary..."

Enter the key from Citylan when prompted

From there you should be good to go. I only extracted the 512 version, but it worked as expected.

Now I'm playing OR2SPJ. I wound up doing this since my 0key is bunk and I can't change my Chihiro region, and the images on Mega are not for my region.
@Finisterre, your process worked perfect with the latest version of mame.

Does anybody have the tool to encrypt a game file back?