If you get my constantly updated M1.XML - I modify all sets to use the most current MAME releases whenever needed. I also make an effort to add newly discovered or newly-added MAME games which fit into the current profiles.
Snippet from my log file:
"Fixes for the Neo-Geo changes until proper undecrypted sound roms are emulated correctly.
I've set up another fake parent, called "decrypt", which you can put all the decrypted roms
that were taken out of MAME in 0.127u5 and u6 for the following sets: jockeygp, kof2000,
kof2001, kof2002, kof2003, matrim, mslug4, mslug5, pnyaa, rotd, samsho5, svcpcb
Again, this will be replaced with the MAME roms as soon as a new M1 core is released that
supports the undecrypted sounds roms."
I did similar things dealing with the c69, c70, c75 Namco Sets - using a pre-existing M1 set with the needed rom as a fake parent to allow usage. All this was the goal of keeping current to the MAME sets.
Download it and give it a try:M1.XML Download Site
Regarding the Naomi/Atomiswave games, if I remember correctly, they do not lend themselves to inclusion into M1. I do remember there being a large amount of sound files being able to be played in Audio Overload. I don't have the link handy for the sound files, though.