And it seems to work. I suppose I can remove FILE_MAN.MO and RAW_REC.MO if those aren't of interest.
File_man is the new file manager module that allows you to move, copy, view, delete files from your storage cards in the camera.
Raw_rec is the raw recording module that I'm sure you have heard about.
If you're not interested in either of these features (or other modules as they become available), sure you can leave them off the card. You can also disable the autoload for each module in the module menu. In this way, the modules can remain on card and if you ever become interested in using them, it's very simple to enable the autoload feature to start using them.
I am unclear about the duplicate AUTOEXEC.BIN. The autoexec.bin from the June 19,2013 NB was about 3.1MB, and the AUTOEXEC.BIN from a43e030494e4.zip was much smaller, about 430KB.
The autoexec.bin in the nightlies is for all cameras. The one from the raw recording builds thread is specific to your camera.
Is this the correct "best practice" ...
If you're already running a nightly, you only need to copy over the files from the download in the raw recording build thread.
I suppose I should check if modules get updated?
If you want to keep the features up to date

Just the same as you would update your nightly build.
I'm not really getting this (I am not a programmer).
Why has it been moved to Modules?
AFAIK, a module works on all cameras. In the future to help keep the code clean, all features that work on all cameras will be moved to the new module system.
Also, my observation is that ETTR-Hint is coupled with the selections for Auto-ETTR, as the selections for "% ignore" and what to clip influence how many EV stops are recommended for exposure adjustment.
That sounds sensible to me. Why should it ignore the settings you have chosen for your tolerance to overexposure?