No text, but a visual code

[ReneZ]

All these questions and more should be prior to any transliteration of the glyphs into letters of the alphabet.

I cannot agree with that. These questions can be addressed very well after the definition of a transliteration alphabet.

why  this obsession with the symbol [c], why the glyph [o ] can be omitted?

Here, I am not sure what you mean. the symbol e is not much different from the symbol i in that it can appear several times in a row. I do not know of any obsession.

The glyph o can only be omitted in very specific cases. This assumes that the term 'can be omitted' means that the omission results in another valid word.
To the contrary, the symbol e can usually be omitted, and the same with several e in a row.
As far as I know, in almost all cases where there are two e 's, one can be dropped leading to a valid word.

Examples:
In the word chol one cannot omit the o . One can, however, omit ch.
In the word chedy one can omit the e. One cannot, however, omit the ch.
(This is all apart from extremely rare exceptions).