In Cine-EI, if I have the waveform monitor on, the EI can't be changed. The numbers themselves will change with the dial, but the actual exposure seems stuck at the native 1250 EI. If I turn MLUT on, the exposure now will change with cycling through the EI numbers, but I can't use the WF monitor.

In the regular Custom mode, the actual exposure changes with the numbers at all times including when the WF monitor is on, but of course, no MLUT available in Custom.

It also seems that in Cine EI, the MLUT is applied (in the lcd viewfinder) even when MLUT is set to off, as when using the WF monitor.

Obviously what I'd like is to be able to use the waveform monitor together with MLUT, for all settings of EI in Cine-EI.

Interesting as well, in Cine IE we can now record at 320EI, thus making possible a 2-stop shallower dof.

This comes at the expense of dynamic range, since the iris would be opened 2 stops into the sensor range.

First of all I did experience some odd behaviour with things not behaving until expected until I did an all reset.

Cine-EI will only work correctly with at least on set of LUT's tuned on on one of the outputs. Any output without a LUT will be seen/recorded at the native ISO. Outputs with a LUT applied will change in brightness according to the EI gain chosen.
This allows you when shooting raw to have the SxS recordings either with EI gain or without depending on your needs.

Changing the EI gain does not change the dynamic range. It simply shifts your exposure mid point up and down within the full available dynamic range. Negative EI gain making the VF (and waveform etc) image darker, so you open the iris in response leading to brighter recordings which results in less over exposure range and more under range. Adding gain makes the VF brighter, so you stop down in response. This then gives you a darker recording so you have greater over range and less under range.

The problem was I had the wrong MLut selected for the viewfinder output, had chosen S-Log2 (same as I was recording) instead of 709 so when I toggled between MLut on/off, they looked exactly the same at 1250EI.

Since you are allowed to make the choice of MLut(s) off and independently select the ISO, I still think it is reasonable to expect the displayed ISO setting to be correct (or grayed out) when MLut(s) are off, just as it is at all other times when MLut is on, or in Custom mode, but I stopped short of calling it wrong, instead asked if it is right.

I performed all reset, but except for the confusing behavior above, have not noticed any problems.