I’m not particularly sure I get your point.
From what you write I guess you have successfully added your files and they’re showing up in your library.
Plex won’t touch your files… however when displaying an episode in your library, it’ll show the season/episode information in a formatted way – this includes not displaying leading zeros (usually users consider that to be “better readable for humans” 
)
Or is this about filebot processing the files and dropping the leading zeroes in your file names?
If that’s the case… here’s some naming template for Filebot described in a different thread:
where /nas/tv/ was the individual user’s folder hosting their tv shows.
