To answer your first question, they do that so no matter what you are called, you can point to the list and "I belong." You can see in my avatar that I have several spellings for each sept in Clan Keith.
The second question... probably more than one man in ancient Scotland named Farquhar.
So how can farquharson be a sept of macfarlane? Unless the website is wrong because I thought Farquharson was a clan in its own right?
Correct, Farquarson is a clan in its own right, indeed it is one of the more active clans here in Scotland, attending games in the north-east, and holding an annual gathering. http://www.farquharson-clan.co.uk/
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