If you do decide to mill the table flat, I would still mill the spoil board flat when attached. If you have never cut aluminum before, you might end up with more problems than 0.5mm. There's nothing super difficult about it, but a bit of experience with it won't hurt, either.
Is it a common way to get X-Y moves parallelism with the table ?
Absolutely. In fact, If were to see a spoil board NOT faced off, it would strike me as rather odd, or perhaps "rookie-ish".