The vowels as we see them today were created by the Ben Asher family and the Ba’alei Mesorah around the ninth century. We certainly had a tradition about how to pronounce everything long before that though. Historians disagree about how many rules of grammar the Ba’alei Mesorah created and how many they extrapolated from Chumash itself. We certainly have cases where the word and meaning stay the same but slight grammatical differences can cause slightly different pronunciations for whatever reason. For example, if you look at the Aseres Hadivros, the Tavs in Lo Tirtzach, Lo Tinaf, etc. gain a Dagesh Kal in Ta’am Elyon which they do not have in Tachton simply because the trop changed.
To answer your first question, as a Gabbai I was told that it is okay to assume that it is Ra’amses in 1:11 only because the language wants to add an extra syllable to the word to end the sentence (not like the Ibn Ezra) so that making a mistake between Ra’amses and Ram’ses would not be something I would need to correct a Baal Korei on (according the Ibn Ezra you would have to correct on that).