Could you elaborate on the last sentence? Wiktionary claims they're pronounced the same modulo pitch accent, but Wiktionary's phonetic transcriptions are (mostly?) auto-generated AFAIK.
塔 can be pronounced as tou, too, or somewhere between the two. It depends on the speaker, speaking style, and possibly dialect. Either way, Japanese speakers rely more on context and pitch accent than actual pronunciation, so it communicates fine.
No it can't, unless someone is spelling it out, or singing it in a song where it is given two notes, or just hyper-correcting their speech based on their knowledge of writing.
Annoyed speech and such can break words into their morae for empahsis, which breaks up dipthongs.
E.g. angry Japanese five-year-old:
ga kkō ni i ki ta ku nā i!!! (I don't wanna go to school!!!)
"nā i" is not the regular way of saying "nai". The idea that "nai" has that as an alternative pronunciation is a strawman.
You're right. I looked up 現代仮名遣いの告示 [0] for the first time, and it says 塔（とう） is officially pronounced as "too". I had it backwards - I thought that 塔 is "tou", but due to the varying sounds of う, people could (and often preferred to) pronounce it as "too" in everyday speech.
This kind of misconception seems not uncommon. There's an FAQ on NHK's website [1] that addresses the question of whether 言う（いう） is pronounced "iu" or "yuu". The answer is "yuu", and the article make it clear that: "It's not that [iu] is used for polite/careful speech and [yuu] for casual speech - there is no such distinction."
I think native speakers learn words by hearing them and seeing them written in hiragana, before learning the underlying rules, so they know "too" is written as とう, but might not realize that とう shouldn't be pronounced as "tou" or いう as "iu". These are at least less obvious than cases like は in こんにちは never being "ha".
Personally, if I heard someone say 塔 as "tou" or 言う as "iu", I probably wouldn't count it as incorrect, nor would I even notice the phonetic difference.
