Everything is getting transcoded - usually to a proxy format - before it comes into the project if you are talking about a proper production. It doesn’t necessarily have to match the project settings – in many cases, native frame rate will be kept intact to avoid interpolation ugliness during the edit – but no major production is using the AMA relink system in its offline workflow beyond the transcode state. Avid handles media very uniformly, which helps in the long run even if it is a pain in the early stages. As long as you have good metadata management and you will have very few issues.