Wow, it sounds more like your trying to keep things complicated, just for the sake of being complicated.
1. Staying AMD actually helps a lot for compatibility with XP. I use a HD4870 and it's pretty OP for most XP era games, even in 1080p.
2. Samsung and Intel, (probably others as well) have released software to allow TRIM and other features to run properly with XP. I have a SSD in my XP rig with no issues. I'd suggest a Samsung 840evo or similar.
3. As long as it's behind a good firewall and you don't have any plans on browsing the web then you should be fine for security, don't even bother with a AV program, just use virustotal or something to scan the files before you install them. (Just make sure the machine is off when your done playing games with it)
4. Virtualization for gaming is just now starting to become possible, and it's not a very good experience yet. I'd stay far away from it if you don't want any problems. If you're curious look up pcie passthough on KVM. Keep in mind that this is only compatible with certain motherboards, mostly just the ones made in the last few years. I haven't seen anyone try this with an older os yet, so I don't even know if XP will work at all with it.
5. I have run into a great number of older games that don't run the same under win7 and up. They may still run, but they don't run the same. This is the main reason I have a XP rig, (I'll be honest it's in my closet collecting dust atm...) this also goes for why I have a PS2 and don't just use the emulator. The difference between XP and Vista was MASSIVE, MS changed basically everything, this was largely fixed in Win7, but 8 and 10 changed this even more. I totally understand why you would want to keep Win XP for this build. especially for the 32/64bit issue.
6. There's no practical reason to choose 2000 over XP. XP was compatible with FAR more games than 2000 was (even win9x games), and there while most XP era games work on 2000, patches and other weird things are required and IMHO that kind of defeats the point of a retro rig. The same can be said with Vista over Win 7. Win 7 was basically just a fixed version of Vista, and is also far more compatible with games. That being said, I've run weird OSes in computers like this just for the LAWLZ. I have a WinME gaming rig that I basically use for a laugh (man it BSODs a lot!).
Overall I see this as you trying to get this build to do far more than is realistic. If you want to use this as a WinXP gaming rig, then do it. Keep it simple and don't try and dualboot it with a newer OS. Use a separate PC for that stuff, you'll save a lot of headaches.
Also I've ran this platform for a while, DON'T use it for virtualization. AMD was TERRIBLE at it before RYZEN came out. It's slow as hell and missing most of the advanced features that would enable a high speed desktop experience with it.
That being said I hope you have fun with this build, and be sure to let us know what you decided and how it all went.