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?