If you are worried about it, call the dealer and ask them what transmission is (not the part numbers, the actual model) in a 2004 Neon and then a 2005 Neon. This is how I've always understood the automatic transmission breakdown:
'00-'01 had the 31TH
'02 had the 41TE (I confused the numbering in my previous post)
'03-'05 had the 40TE, though, the 41TE would technically be an "upgrade."
However, Dodge manuals state the '03 had the 41TE and the '04-'05 had the 40TE. Going by their parts manuals, the '04 and '05 were the only '03+ ones to have the same transmission.