Success! After a bit of struggling I managed to get a very nice
(night to day) timelapse with clean shadows and almost not clipping in the highlights.
USED 5D3 + ETTR + DUAl ISO
ETTR settings:Trigger mode. Always on
Slowest shutter: 32"
Highlight ignore: 0.5%
Allow clipping: OFF
Midtone SNR limit: 6EV
Shadow SNR limit: 2EV
Link to Canon Shutter: OFF
Link to Dual Iso: ON
Shadow metered areas: OFF
Show debug info: OFF
Dual ISO (enabled)Intervalometer:Take pic every: 1m, Start after: 3 sec, Stop after: Disabled, Manual FocusRamp: OFF
Post Deflicker: Sidecar file type: Adobe XMP
Deflicker percentile: 50%
Deflicker target level : -4EV
The modules performed very well automatically without any human intervention. The only thing I noticed is that when Dual Iso kicked in, there were some images that alternated between DUAL ISO 100-200 and no DUAL ISO. After a while the system stabilized and all of the photos thereafter where DUAL ISO.
POST-PROCESSING with XMP slidecar files (ACR and Photoshop required)This proved to be the more difficult part since the
exposure compensation is not passed through the cr2hdr process. Maybe this can be updated in a future release making this process a slicker deflicker.

1. Open all the CR2 files with ACR (xmp files will adjust the exposure) and save them as DNG.
2. Process all of the DNG with cr2hdr
3. Change the extension of all DNG back to CR2. Make sure the xmp files are put back with the CR2
4. Open the CR2 with ACR (again) and save them as tiff, this will adjust the exposure of the tiff files by the deflicker exposure. Save then to a separate folder. Make sure that the exposure compensation is applied in ACR.
5. In Photoshop create a small action to open a file and change the canvas to the correct size of 5760x3840, then save the file. This is required since the cr2hdr process is increasing the size of the images to 5796x3870.
Again this is something that may be able to program in cr2hdr so that the output images do not change in size.6. In Photoshop open the Batch command (in File, Automate) and select the action you created by selecting the Set and the Action.
7. Click on Source and select Folder.
8. Click on Choose and select the Folder where you saved the tiff files.
9. Select the Override Action "Open" Commands
10. Select the Override Action Suppress file Open Options Dialogs.
11. Click on Destination and select Folder
12. Click on Choose and select a folder for the new tiffs
13. Select Override Action "Save As" Command and Click OK.
14. When needed the images are automatically re-sized , you can import these tiffs in your favorite video editor.
Technical Notes;I also tried sending all the cr2 files directly to the cr2hdr which converted the DUAL ISO images to DNG. Then rename all the DNG back to CR2 and then along with the xmp open the cr2 to save as tiff. The problems is that the converted DNGs (converted to CR2) in this manner will never accept the exposure compensation from xmp file. I tried and tried and could never get them to accept the deflicker exposure.
There are a couple of places (1. and 4. above) where you can adjust shadows, highlights, etc. I only use tonal curve in ACR to avoid flickering.