Maybe I misunderstood something in moteino schema...
With moteino (mine si R4 but I think there's no difference in power supply with R6), if I want to use an extern 3V3 power supply (or other supply less than 3V3), I unsolder the LDO, then I connect my extern 3V3 to 3V3 pin analogside header.
PWR from analogside header is connected to PWR pin from FTDI header, but disconnected from everything else. So to upload a sketch, we need to supply 3V3 on 3V3 pin even if FTDI is powered by USB. But apart from that, there's no difference.
In normal use, PWR pin becomes useless.
So, to reproduce this state with LDO still on PCB, if we cut the VOUT pin of the LDO , we will be in the exact state as if LDO was removed, apart from LDO will run without load when FTDI apply power on PWR pin. In normal use, if we let PWR pin on anologside disconnected, LDO will be connected to GND, but nothing else.
So, apart from 3V3 pin which become a power input instead of a power output, I don't see where is the risk for the MOTEINO, apart from applying 5V on 3V3 pin, but it's already the case.
But anyway, a moteino without LDO is ok, it's less universal to my mind but I probably miss the problem you guess.
On your exemple, I don't isolate 3V3 pin header from VCC, so 3V3 pin is still an power output with LDO, with a simple jumper, but if you think it's a bad idea, it's probably than I miss something, so don't worry, if you want to spent some time to explain to me the problem, you're welcome, but I guess you have more intersting things to do.