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Unicode: Unaswered questions

Isn't using CGJ a dangerous thing? Because, a document (eg: a wiktionary.org document) written by multiple people using various inputting tools can quite possibly have different 'spellings' for a conjunct or word, without reader or writer being aware of it. This can cause many problems including ineffective searches and inconsistent collation.
My understanding about collation value of a codepoint is that it is directly tied both ways to search/sort functions. That is, searching and sorting is done using collation value and when collation values vary, search/sort can potentially give different results. Does collation value has any other purpose? If no, then by attaching search and sort meaning to ZWJ, aren't we actually adding a collation value to ZWJ? That is, ZWJ in turn becoming ZWJ + CGJ in case of chillus.
What was the reasoning behind giving vowel signs a different codepoint? Why they weren't encoded as, say, VIRAMA + AA = sign of AA
When do you say two words with different orthography and same meaning have two different spellings. Example: color & colour. Same way, can we say that the old and new orthography renderings of the same word, say /Sabdam/ (meaning 'sound'), qualify for two different spellings?
What is the assumption Unicode makes about the input methods? Does it assume the input method has word lookup feature or just a basic keyboard layout or inputting each Unicode codepoint by codepoint?

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