Long and short vowels must obviously be distinguished. I think either yōko or yooko are fine. Either Tōkyō or Tookyoo will let a beginner pronounce the word correctly. Some prefer youko and it works fine in almost all cases too, but perhaps there's no real value in clinging to the accidental way with which hiragana happens to represent long vowels; it isn't inherent to the language. Besides, there's a small added benefit in disambiguating real [ou] pronunciations like omou.
Your point about visiting Japan is well-put. There's no arguing with the fact that anyone who wishes to understand Japanese should learn kana and kanji. But I think that there's a real value in putting emphasis on the spoken language first, and a well-developed minority tradition of teaching Japanese like this in a serious manner, not as a crutch. E.g. Eleanor Jorden's JSL textbook follows this principle, as do a number of other textbooks and guides.
"To get started in learning to read modern Japanese along the correct lines, it is essential that first of all you have some knowledge of the modern spoken language. This is so important that it is well to emphasize it strongly from the beginning - contrary to what you may think, you undoubtedly will not make the best progress in learning to read Japanese by starting in your study of the language directly with reading and writing in the Japanese script. Some previous work with spoken Japanese is essential, and the better your grasp of the patterns and the forms of the spoken language, the faster and surer will be your progress with the reading materials in this book" (Roy Andrew Miller, _A Japanese Reader_).
But that is not currently the case in the most popular romanization method (Hepburn). 日本式 is the "better way" for learners but Hepburn is used for foreigners and learners because of how prevalent it is.
The two largest grammar guides that I see shared in /r/learnjapanese, and on the internet in general, are imabi.net and Tae Kim's Guide to Learning Japanese. Both of which advocate studying Kana and abandoning ローマ字 ASAP. The first result for "learning japanese" is Tae Kim's guide and on one of the very first lessons it even opens with this comic [0].
I take the quote you quoted more as "Don't try to learn Japanese grammar by reading a Japanese grammar book" and less as "Don't try to learn Japanese grammar in English but explaining the fundamentals using Kana." It talks about all reading being in Kana/Kanji rather than just the important bits.
Unless your object is to learn writing, specifically, why is it important? It's like learning homophonous spellings in English -- it has no bearing whatever on the spoken language.
Tae Kim has put together a nice site but he's an amateur without much knowledge of linguistics.
I actually think this is because our opinions differ. I'm running under the assumption that "learning Japanese" involves all aspects, spoken and written. You're running under the assumption that "learning Japanese" involves only being able to speak the language.
You're correct. If someone's only goal is to learn to speak a language - then they don't need the writing system and can use romanizations with little issue. However, when (not if) they decide to learn the writing system they're shooting themselves in the foot and doing themselves a disservice. They may not decide to learn the written form for an entire decade, but if they ever live in a country where they need to use the language on a daily basis - the country isn't going to change all their signs to romanizations of the language just so they can find their way around town.
You've rather misconstrued what I'm saying. I object, specifically, to the idea that the writing system determines pronunciation. It's also less than clear (it is contentious among educators, at any rate) that learning the writing system first is the best way to learn Japanese -- although, hey it worked for me.
If you want to argue that you have to learn the writing system that Japanese people use to read and write Japanese and hope to have people understand you, well, of course that's true, but it's so blindingly obvious I don't know why you feel the need to argue about it.
> the country isn't going to change all their signs to romanizations of the language just so they can find their way around town.
Probably a bad example since you have to go pretty damn far afield before the signs aren't all also in the Roman alphabet.
Also, nobody says "x-go ga sittemasu" to mean "I know such-and-such a language."
No it isn't. It's because those sounds do not appear in the same positions in English. These arguments are both tired and completely ignorant.
I disagree entirely. ローマ字 is a terrible trap for beginners and it does affect their pronunciation. It is why so many people struggle with the Japanese "r" and つ. It is why people pronounce "せんぱい" incorrectly. Do you see it romanized as "senpai" or "sempai"? Both of those differ greatly for beginners. It is why they learn 言う incorrectly. It is always romanized "iu" though it is pronounced "yuu" and unless you are told or are listening to how natives say it, you will learn it wrong.
Should ようこ be romanized as "yoko", "youko", or "yōko"? Would you read any of these differently from one another? The answer should be "yes" because よこ is not equivalent to ようこ but in some romanizations you will see them be equivalent.
It's a big wake up call when you visit Japan and realize you're completely illiterate outside of English signs (if you are in 京都 or 東京). If you did not study Kana you will not be able to read anything. My first recommendation for learners is to learn Kana and completely abandon romanizations entirely.
E: Speaking of 東京. Is it romanized "Tokyo" or "Toukyou"? Which of these do you think most people, including learners, see it as? Can you see how they end up pronouncing it incorrectly because of how it is romanized?