welcome to the forum.
interesting post. i'll share my thoughts as a non-muslim. (some non-muslims here stick their noses in to everything )
i agree with you - the qur'an is not a science book and was not meant to be.
if you believe it to be the word of god - that should be quite sufficient in itself.
science and religion are 2 different systems. it is not that one is true and the other false - they are just different. religion needs (and really can have) no proof - this does not make it unreal and does not need to be taken as a weakness.
i see these kind of arguments here all the time and it seems like some muslims and some atheists (often the same people, lol) can go round and round and round over the same old stuff and (of course) get nowhere. and it is all so pointless.
i also agree with you that when muslims use this argument, it makes them look foolish. similarly when muslims argue that pig is haram because it isn't healthy. both open the way for mockery and silly arguing because the muslim argument is weak and the atheists happily come and pounce.
the qur'an often points out various natural phenomena, saying they are "signs" - and they are indeed to those whose hearts are open to it. and that is enough.