When words are borrowed in speech, they're generally "repaired" to match the phonology of the target language. In Japanese, that usually means picking the nearest consonant and vowel sounds and adding epenthetic vowels to avoid consonant clusters that aren't allowed (like /str/ → /sutor/), although other methods of repair are occasionally used (e.g. deletion).
But this isn't an exact process. It depends on the pronunciation of the original word (which may vary) and the way the word is perceived in the target language (which may also vary). Sometimes more than one repair is possible, and sometimes words are borrowed more than one way: consider strike ストライク and strike ストライキ, or Hepburn ヘボン and Hepburn ヘプバーン, as in James Curtis Hepburn and Audrey Hepburn.
And of course, there are further complications. Many words are borrowed via writing rather than speech, and words have been borrowed at different points in time, resulting in different pronunciations than you might expect. Most speakers no longer say the /h/ in white /hwaɪt/, but it was relatively common back when ホワイト was borrowed.
Let's look at your examples.
In the case of time-out and backup, we can see that each word corresponds rather transparently to a pair of words, time out and back up. I suspect that this correspondence influenced both words, whether they were borrowed via speech or writing. What's more, both time-out and backup can be pronounced like a pair of words in careful speech. Given that, the way they're borrowed makes sense.
I think that pineapple is less transparent (despite the spelling) and that most speakers pronounce the /n/ as a syllable-initial consonant (following the maximum onset principle), like "pie napple" rather than "pine apple". Honestly, the reason this word in Japanese doesn't match my expectations as an English speaker is the location of the pitch accent, not because it has ナ in the middle.
A couple of your examples are implausible. Menu simply doesn't sound like メンユー, it sounds like メニュー. Try saying it both ways! And there is no separation to "remain separate". Piano doesn't sound like ピャノ. The vowels are fairly distinct in English and I see no reason why a Japanese speaker would perceive them as a glide or interpret the spelling as representing a glide.
But I'm not sure it's really possible to answer a question like this rigorously. I see no reason why 'W' double-you couldn't be ダブル・ユー as well, but whoever borrowed it first must have perceived it the other way and ダブリュー became more popular. For that matter, I don't see why time-out couldn't have been borrowed as タイマウト. It's not an exact science and I'm afraid there are no absolute rules to explain it―all we can really do is try to find tendencies and patterns.