considering modern Filipino borrows various words that won’t work well with the alphabet.

This is concerning to me as well. I hope there would be a standardized, modernized version of baybayin that is maintained by some governing body (not necessarily a government body, it could be a committee composed of academics and scholars) that would sort this kind of issue, and a lot more (such as how it can be supported on computers and smartphones). Text entry is also an issue I want to be standardized (providing a set, or several, of standards on how text entry should be handled).