Ines, thank you for the in-depth response. There is a lot here to digest and look into. The HN thread was an interesting read. What stood out to me was the distinction between an "application" and "library".
In the case of prodigy, I find that it fits neatly in the application grouping: a cli app that helps you annotate and manage data with an intuitive GUI and fits nicely into a data preparation workflow. Where as something like spacy is clearly a library that you incorporate into your app, so shared dependency flexibility is super important.
In a previous project, we opted to use pyinstaller to deliver an app. The size of it was not an issue, but it quickly became very cumbersome when we needed to specify hidden imports and static data. This often occurred with data science packages that relied on underlying C libraries.
Also, thank you for the pex recommendation. I have yet to use this and am looking forward to giving it a good look 