In Chinese language, it may be the same for other languages but I am not very sure so shall not comment here, similar or even identical words can have absolutely different meanings that are imposed due to the context or environment in which they are in. So, speak and write with care and after much thought if you do not want to have communication breakdown.
The H*nyu P*nyin which we nowadays use was something which was passed down to us from Ch*na after all the proper legislative and administrative procedures have been done. It is unlike the general misconception of being initiated by W*estern countries. It was put in place to help the kids in Ch*na to master their common Chinese language better, and also to help the people from other dialect areas to master the common Chinese language better and faster.
A lot of language rules, principles or guidelines put in place by the academics with regards to Chinese Language is far from being perfect and all encompassing. As the use of language is constantly adapting and there are always abnormal uses that people commonly use, there will always be new theories, be it improved or creative ones. Thus a lot of things which we learn, especially at the tetiary level, is susceptible to change. But, change is the only constant afterall. ;)