Firstly, TJones, you're doing an incredibly good job in a very difficult task. Well done and thankyou.
I am no expert in Khmer script, after spending four years half-heartedly learning to read, write, and speak it. But I'm sure I'm better than nothing.
This section looks like it is all typos to me. And your assumption about incorrect syllable boundaries is correct.
The characters following this កុ in this កុែំ do not belong after the syllable កុ on their own and are not connected to it. They are the start of the next syllable or word and missing their consonant.
Your interpretation of this one looks correct:
ញុាំ ( ញ + ុ + ា + ំ ) | ញុំាំ ( ញ + ុ + ំ + ា + ំ ) |
The word means to eat.
But as you discovered in the "Original is More Common" section, there are multiple ways of typing this. It is possible that there is not actually a correct key sequence and that it is a matter of "if it looks right, then it is right"
ញុាំ ( ញ + ុ + ា + ំ ) | ញុំា ( ញ + ុ + ំ + ា ) |
I believe your interpretation of this one is also correct:
ឆ្មាំ ( ឆ + ្ម + ា + ំ ) | ឆាំ្ម ( ឆ + ា + ំ + ្ម ) |
This is because the subconsonant ( ្ម)m follows the consonant (ឆ)ch when spoken and the vowels follow that.
Questionably Reordered Syllables
There are some incorrect syllable boundaries in here. But there is also a problem where the subconsonant has been typed last, instead of directly after the initial consonant. I can't think of an instance where within a single syllable anything gets between the initial consonant and its subconsonant.
The original in this one is a commonly used syllable at the start of a word. So my guess is that the following syllable is missing its consonant.
កុេំ ( ក + ុ + េ + ំ ) | កុំេ ( ក + ុ + ំ + េ ) |
Basically, if it fails to render, then it is incorrect and probably a typo.
Visible Duplicates
I'm pretty confident that these are all just typos.
Duplicate Supplementary Consonants
Subconsonants in Khmer do get stacked up sometimes. I've got a feeling that I once saw one that was a stacked duplicate but my memory is very vague there. If I did, it was probably dealing with an introduced word.
Where there is a consonant that is typed, but it doesn't render, I'm going to deduce that it is always wrong because what is the point of typing a character that is never seen?
ស្កូ ( ស + ្ក + ូ ) | ស្កូ្ក ( ស + ្ក + ូ + ្ក ) |