Not really. A flask is a special type of bottle. "Flasche" just means "bottle".
Flask can also refer to any type of bottle actually, but it is a rarer usage, that many native speakers will have rarely heard used. It sounds 'older', and so is sometimes used ironically if one is pretending to be aloof.
"Hand me that flask of wine, my dear fellow, wot!"
Flasche is non-specific. It means 'bottle' of any kind. A baby bottle would be Babyflasche. A water bottle would be Wasserflasche.
I think the answer is that the German "Das ist ..." is more or less like the English "It is ..." It is used no matter the gender of the thing. Of course English does not have gender like German, but think about a doctor that first tells a couple the sex of their baby; "It's a boy" or "It's a girl". In that sense, I think "das" does not decline.