Your premise is wrong. Homographs that are not homophones exist in a great many languages, and in a great variety of writing systems. Germanic, Slavic, Sinitic; Latin, Cyrillic, Hanzi; you name it.
To distinguish lead from lead, 易 from 易, замок from замок, Heroin from Heroin you have to rely on context. Some languages might try to help you out by using diacritics (Spanish, French, Greek) or stress marks (Russian), but others will not (Modern German, Modern English).*
When there's not enough context, all bets are off, but keep in mind that that is not some weird exception, but rather the default situation. Any sequence of characters in any language is free to have as many different meanings as people choose to give it, and is thus prone to being ambiguous with not enough context provided. (And remember how there are complete homonyms, where not just the spelling but also the pronunciation are identical. Yet everyone makes do with them just fine.)
Present vs. present is an example of an initial-stress-derived noun, which are extremely common in English. The thing is, these homographs in particular are exceptionally easy to tell apart, because one is a verb and another is a noun. You'll typically need very little context to tell what part of speech you are looking at.
As to read, it actually nicely demonstrates another problem still: we likely have the pair of homographs because otherwise we'd have a pair of different homographs. That is, the past-tense read actually used to be spelled "red", but that in turn conflicted with the adjective red. We have prior questions on that.
* And of course at the extreme end of this spectrum you have systems like Japanese, where every single kanji has two readings, by design, so as a complete layman I can't possibly tell how to read anything at all, until some kind person comes along and spells it out for me in hiragana. Yet lo and behold, the system is alive and thriving, and has been forever, and will go on to outlive me.
You are right, garage is a French loan and at first pronounced in the French way. After some time such words are pronounced in a way that is more conform to English pronunciation.
OALD has three pronunciations for BrE (stress on the first syllable), and two for AmE (stress on the second syllable). Normally the most common pronunciation is given first. So in BrE the French pronunciation is still the most frequent.
http://www.oxfordlearnersdictionaries.com/definition/english/garage_1?q=garage
Best Answer
The vowels represented in most European lanaguages (but not English) by /a/, /o/, and /u/ are back vowels: in pronouncing them the tongue is positioned back toward the throat. The vowels represented by /e/ and /i/ are front vowels: the tongue is positioned toward the front of the mouth.
The /k/ sound represented by Latin /c/ is articulated with the tongue at the back of the mouth. When the syllable /ka/ or /ko/ or /ku/ is uttered, the tongue doesn't have to move very far, if it all. But with the syllable /ke/ or /ki/, the tongue must shift rapidly toward the front of the mouth. The same is true with the voiced consonant /g/.
Consequently, there is a physiological tendency to alter the pronunciation of /k/,/g/ before /e/,/i/—to position the tongue further forward for the consonants in anticipation of the following vowel.
At some point during the Late Roman Empire this colloquial palatalization (reinforced by similar movements of other consonants) became the “accepted” pronunciation. /k/,/g/ before /e/,/i/ became /tʃ/,/dʒ/, evident in modern Ecclesiastical Latin. The pronunciation changed, but not the spelling: for to change the spelling would cut writers and readers off from their literary heritage.
These pronunciations were inherited (and developed further) by Latin's heirs, the Romance languages. And in due course they passed to English. When English literature revived a century or so after the Conquest, its writers were employing a language greatly enriched by French lexicon and were addressing an audience for whom the “literary” languages were French and Latin. These writers naturally adopted French orthography, and its distinct front and back pronunciations for /c/ and /g/.