That is such an interesting question. You are right, it does mean perfect, but I would say it underlines the perfection of something by drawing attention (as the word suggests) to the lack of imperfections (i.e. flaws); thus it often refers to something one might expect not to be perfect:
She has a flawless complexion. (Quite a common usage.)
His English is flawless.
Flaw, incidentally, is a useful word in its own right. You might come across the expression: a fatal flaw, meaning the imperfection that destroys somebody in some way ('According to Shakespeare, pride was Julius Caesar's fatal flaw.') A faulty argument is often said to be flawed.
Yes, you can use perfect in very much the same way, but they don't mean exactly the same thing or there would be no use for another word. Like I say, flawless has the additional nuance of looking for or expecting imperfections but finding none (we are talking very subtle nuances here). Excellent, on the other hand, means very good, but not necessarily perfect:
They examined the diamond and found it to be flawless.
His English is excellent but he still makes the occasional mistake.
Sorry this is so complicated! It seems to be the way of languages that the more you examine a word, the more slippery it becomes; though that is the joy of them also!