Well, it's certainly true that "e" for [i] is almost unique to English.
But it's pretty common for languages to preserve phonetic distinctions in their orthography that have disappeared from the spoken language—Latin American Spanish has silent "h", "z"/"c"/"s", and "b"/"v", so "Helvecia" would be pronounced exactly the same way if it were spelled any of "Helbecia", "Helbezia", "Helbesia", "Helvezia", "Helvesia", "Elbecia", "Elbezia", "Elbesia", "Elvecia", "Elvezia", or "Elvesia", and if you think "Helvezia" is impossible I refer you to "azimut", "zinc", and "enzima". And on my local blacksmithing group on Fecebutt I regularly see people spelling "haber" as "aver". Not to mention "k"/"qu"/"c"—no reason "cuákerismo", "folklórico", and "kilovatio" couldn't be spelled "cuáquerismo", "folclórico", and "quilovatio", but they aren't. ¿Kesesto? https://www.youtube.com/watch?v=u4DbC1rbERg
In the other direction, it's pretty common for languages to have more vowels than the Latin alphabet, like English's 13 or so (14 in my idiolect). Even Latin itself had 10 vowels. There are several different ways to handle this problem: you can just hope people guess the right pronunciation from context (like modern English and classical Latin, though modern transcriptions of classical Latin often have macrons to help you out); you can use digraphs, as in "floe" and "each"; you can use a different alphabet with more vowels, like bopomofo (12 or 17 vowel signs, depending on whether you count codas that include consonants) or Cyrillic (9 or 13 vowel signs, depending on how you feel about diacritics) or hangeul (10, 21, or 22 vowel signs, again depending on how you count); or you can use diacritics, as in Portuguese "à" [a], "â" [ɐ], "ã" [ɐ̃], "à" [a]. Or some combination.
Speaking of Portuguese, though, many dialects of Portuguese are an exception to your generally excellent rule: "livre" is totally pronounced [livɾi] in, for example, Rio Grande do Sul. This is made more complicated by the fact that in stressed syllables it's totally [ɛ] and not [i].
I think [ɛ] "90% of the time" is an exaggeration given that only 86% of people are non-Chinese, and Chinese is another exception; as noted in the original article, "e" in hanyu pinyin is [ə], as in French (another 1% of people). But [i] is a very rare value for "e" outside English.