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Hmmm, interesting. I'm thinking in the reverse way.
1) Not a big deal to cut the connector, and connect directly into the screw terminal in the DC-DC converters or the Relay
2) I agree with this. But because the cooling fan it will be collect dust anyway
3) It's not an issue for me, I have 24V led strip. But for this aim maybe I'll use XT60 too maybe
4) Yeah, it could be tricky. You can't absolutely remove the box because the tons of connectors in the motherboard, but definitely could be trick if you have a fixed connector in the right box too.
To be honest, I simple don't trust this XT60 connectors. I can't belive it can delivery 60 amps, but 30 either. And this PSU give around 16amps at 24V at full load. This is why I prefer to skip this connector where the current is bigger. I worked with higher voltage too, a 60amp connector looks much more powerful. For example the typical German style wall outlet designed to 16amps, and the connector there much more bigger.
I still wait for the new motherboard, rpi, etc etc, I have time. But maybe I'll create a remix from your work and skip these XT60s (or at least at the main input). From other hand, thank you for your work, it's pretty impressive and contain every important feature which missing of the original box.