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."
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.
[0] http://i.imgur.com/A5vxfio.png