I read it the same way. It seems that 丸ごと places emphasis on ‘completely’ with a nuance of ‘without modification’ or ‘in its original form’. It’s more about no part being cut out or excluded than filling an entire space. (To put it another way, it’s pretty obvious what an ‘apple’ would be as a whole/without modification; it’s less obvious what a cake would be in such a case, especially since we don’t even know what sort of cake this is.) I’m not really convinced that it can mean what the translation implies. At the very least, such an interpretation would be unusual, whereas I found cake recipes on the Japanese Internet that involve whole apples when I searched the example sentence.
Anyone else have any other thoughts? Should we tag the mods to ask the WK team to look into this?