Lyric discussion by Malkmusian 

Cover art for Flash Gordon's Ape lyrics by Captain Beefheart and the Magic Band

Basic lampooning of pop culture icons King Kong and Flash Gordon, done in the typical Beefheart style.

It's obviously meant for comedy - nothing truly astounding behind the lyrics.

My Interpretation

No, I think it's a deeply sceptical song about scientific arrogance and the cluelessness of the human race. "Flash Gordon's Ape" references science fiction but points out that for all our pretensions we're still only monkeys, and a little knowledge is a dangerous thing.

@Malkmusian Losttango's answer is right. Amusing point - "too day" is what Don would say when reluctant to venture out into the hot desert sun.
Again, it's worth finding the bootleg of the band playing the backing track - to hear what's actually going on behind the tenor/soprano sax outpouring!