Indeed, said modulations are the focal point of this piece, the base material from which its structure was designed and its counterpoint woven. I am unsure, however, on what you mean by "justified and needed by the music/melodic line", since the level of contrapuntal constraints required for a 5-voice setup was main guiding force behind the final resulting contours the melodies took, aside from the proper individual construction thereof.
I trust that most professional choirs out there would be able to instinctually find favourably specific moments within the piece to strategically insert breathing commas, such as phrases ending in a half note giving ample space for singers to momentarily stagger their breathing, just as you said. As for the sense of breathless artificiality you mentioned, I suppose it must be a matter o subjective relevance, since it comes off neither as "artificial" nor awkward in any way for me as long as the performing choir can handle it properly, as I hope will be the case under most circumstances.
Regardless of our disagreements, I can only thank you for your thoughts, criticism and kind words, as there will most likely always room for improvement in my compositions no matter how hard I try to perfect my technique and integrate all aspects in which I may find myself lacking, so as to get them as closely as possible to second-nature for me and, by extension, my art.