In all the years I've talked to front office folks about players/prospects, I've never seen them have the concerns over log jams, roster crunches, players being blocked, promotions, etc. These are concerns of fans and I've yet to see front office type stress over any of it....they are manufactured "problems" for the most part.
Priority prospects get handled first....this goes with season-opening roster construction and in-season player movement. If a priority prospect needs a specific assignment, they get it....end of story. When the team decides to promote -- for the purposes of this, let's say McGonigle -- then they promote him, and the underlying decisions are quite black and white or obvious.