Omigod, is that ever a can of worms.
The usual transliteration, which I used on my flashcards (and in my upcoming book), and which is used on Wikipedia and in many textbooks, should be taken as phonemic only. Scholars think in terms of the names given in the Masoretic tradition.
When you ask how BH was pronounced, you have to specify which BH? There are basically three answers:
* How modern Jews pronounce it. This can be divided into Ashkenazi and Sephardic traditions. Naturally, these are highly influenced by European languages and Arabic, respectively, and are not how Biblical writers pronounced the language any more than modern pronunciations of Latin are faithful to Cicero. Plus there's the modern Israeli pronunciation which is something of a compromise.
* How the Masoretes who added vowel pointings in the first millennium pronounced it. A complication here is that European Jews (and the Christians who learned Hebrew from them) did not actually know any Masoretes, and therefore interpreted the pointings according to their own contemporary pronunciation.
* How the Iron Age Hebrews, or for that matter the Exile writers, pronounced it, 1000 to 1500 years before. Obviously this has to be reconstructed.
Fortunately one of the best modern discussions of all this is online, that of Geoffrey Khan:
https://www.ames.cam.ac.uk/publications ... cal-hebrew
(Fortunately for Khan, the Masoretes actually wrote a lot about the vowels. But they wrote in Arabic, so this didn't get communicated to the West.)
As to your specific question, my understanding is that proto-Semitic long vowels are mostly preserved in Hebrew, but short vowels can be kept, lengthened, or reduced to ultra-short in complicated ways. The grammars I've read are quite conflicted about how exactly length worked (or didn't) in the Masoretic tradition. (Some think vowel length didn't matter at all; Khan thinks all vowels had length variation; Benjamin Suchard has long vowels /ī ē ɛ̄ ō ɔ̄ ū/ and short vowels /a e o/....)