Right - I'll back-track a little...
For this kit both 12V & 3.3V are generated locally or supplied 'directly' via PCIe. So, forget my previous comments about treating 3.3V differently to 12V. If you're going to power this board via the HSMC you will have to supply 12V & 3.3V.
Will the board be happy with this? In short, I think so.
The LTC4151 current monitor might see a 'negative' current through R64. However, given the only loads on 12V_OUT are U15 & U19, the current drawn will be tiny, around 1mA. Across that sense resistor that doesn't amount to enough to register a current in the LTC4151, assuming it can report negative currents at all (I don't think it can).
I don't know, but I'd be very surprised if the MAX controller was designed to shut the board down under these conditions. High currents - OK, maybe.
When the board is powered via the PCIe connector (with U35 switched off via power switch SW1) U15 is active and U19 is not. In the same way D45 becomes active (for 3.3V) and D44 is not. Both LTC4357 & LTC4352 are designed to work in a system where they are off permanently. When off they ensure power isn't fed back through their respective FETs.
Connecting power in the way you want will see all four of those parts remaining off (due to lack of power from either U35 or the PCIe connector), which in turn will hold their respective FETs off, preventing any back powering of the circuitry on page 21.
So, I think (disclaimer: read that again -
i think) powering the board via the HSMC will be fine and you'll be unlucky if the MAX system controller shuts the system down. If it does, I suspect we could work around that...
Let me know how you get on.
Cheers,
Alex