I guess if I find a better one, then I could trade it.
That would probably not be a straight swap.
Going back to your wish list ...
I’d like to get 64GB of RAM
There is nothing stopping you from putting 64 GB of RAM in your MP31. It will work just fine (subject to optimisation) and you can ignore the official spec sheet that says otherwise because it was quickly found that high density RAM works at 64 GB. There is a thread somewhere on this forum that outlines this. The RAM speed on the MP41 will be faster but you need to try a web search to see whether it will make a noticeable diffference.
That one is a bit vague. What exactly would a Nehalem processor bring to the table for you? I might be wrong but AFAIK, it is basically a half step upgrade between the CPU Generation in the MP31 and that in some MP51. I believe it does have Hyper Threading, which the MP31 does not.
native macOS High Sierra (via flashing), and OpenCore.
This and the one following appear to be limitations you have encountered with your MP31.
HiSierra is not supported on MP31 but you can use a DosDude patched instance or better still, use Opencore. You will then need APFS support which MP31 does not have. HiSierra can be installed with HFS+ but probably better to sort out the APFS thing out.
DosDude instances can provide primitive APFS support. It is possible to instead hack your firmware to add proper/full APFS support. This is very much doable if a bit risky ... certainly a hair raising experience.
I haven't seen any reports of anyone damaging their firmware when following the instructions but it is a distinct possibility.
My suggestion would be to simply implement the MyBootMgr process in my signature which will set RefindPlus and OpenCore up for you without mucking about with your firmware. RefindPlus will then automatically supply APFS support every time you boot up.
I also have an NVMe card but when I tried hacking it onto my 3,1, I got kernel panics. Not helpful especially without a boot screen. If I got the 4,1, I would keep the old graphics card and buy a GTX 680 and then flash it.
MP31 does not support NVME, hence the KP. You can also hack your firmware to add NVME support but once again, RefindPlus will automatically provide this.
If I got the 4,1, I would keep the old graphics card and buy a GTX 680 and then flash it.
I think your RX560 is better. As for boot screen, RefindPlus and/or OpenCore will give you one with that GPU. Bear in mind that this is a GPU that can go beyond HiSierra easily. Why stop at HiSierra when people are running Monterey on MP31? I do think BigSur is the higheset MacOS target to go for at this point and the GTX 680 will also do BigSur but the RX 560 can go beyond more easily.
Back to the better unit thing, the attraction of the MP41 is that it can be flashed with MP51 firmware, which would give you an easier use path, in that there is more community support available for MP51. This is not trivial depending on your abilities but the deal you had on the table did not look to be particularly appealing once cold logic is brought to bear.
My current judgement is that MP31 to MP51 look set to bite the dust in terms of usability on new MacOS at the same time. The next release will be yet another test of this. I believe that even if the MP31 chokes on the next MacOS version and the MP51 does not, it is unlikely the MP51 will be able to go further than that version, with a high chance of it choking on some mid point release of that version.
Only other thing is the MP51 will be 'x' years newer than MP31 which may impact on component reliability. I do think they are all together in the "can fail anytime" zone but the difference, even if small, is there.
All this makes the Mid 2012 the one to look for if wanting to trade up ... especially if it has the real Westmere CPU upgrade and not the Nehalem pretender. This, as said, is not likely to be a straight swap for an MP31.