It's the emphasize. If you want to focus on 'that apple' then it'll be "Apel itu"
If you want to focus on 'that is (an) apple' then you can say, "Itu apel"
But for me (as a native speaker) yeah, we don't really mind about it. You can say both sentence for daily life.
For example :
"Ini apa?" (What's this?) "Oh, itu apel" (Oh, that's an apple)
"Apel itu warna nya apa?" (What's the colour of that apple?) "Hijau" (Green)
Well I hope you understand, I'm not really good at English but I hope you understand what I mean
I am finding that this program, puts the words in a sentence that you have not even learnt yet! Making it impossible to get them right. Also it would bd handy to explain some of the language before it starts. That way you woulc know you say it back wards, and that eords are added in and out as they desire.