I tend to think that Pearl's "I DO like pie" line was more out of character as she recognized the sexual innuendo and went for the dramatically ironic confession so soon after being baffled by the butterfly pun rather than an inconsistency about her feelings about food. But in retrospect it does appear that she is probably obsessed and romantically frustrated enough to make the oral sex double entendre without catching any of the other jokes or even considering her feelings about actual pie.
The oblique reference to the human centipede - which was lampshaded in Giant Woman and page 7 of the Zine didn't really need to be parsed out. It failed as a joke in Fusion Cuisine because it is really just gross out humor based on references that don't necessarily connect. Nevertheless the joke is that Pearl is completely creeped out by the whole process of eating (even normally) in spite of symbolically being the least punished 'head' of the human centipede-like fusion - while Amethyst's response is pretty much 'fuckyeah! If it's in a horror movie sign me up!!!'
Pearl is clearly horrified by the most benign biological processes and Amethyst is downright thrilled by body horror. Neither of them is meant to 'get' the nuances involved in biological living or have a reasonable view about food - instead they express opposing views and argue about it. Steven's entire existence might be Rose's attempt to force them to develop an understanding and appreciation for the details of biological life. Rebecca Sugar described the show as being about a love affair between the magical/sci-fi creatures and the mundane.
But when it comes to the whole awkward fan response to "I like pie" I can't help but wonder why fans didn't similarly fixate on the idea that if Amethyst had REALLY seen Greg's 'junk' then shouldn't SHE have remembered the laser light cannons?
This is children's animation. Sometimes a cigar is just a symbolic penis.