I wonder that just the factory presets of Flextone and PODxt differ so much.

Line 6 says "The all new Flextone III features 32 fanatically modeled amp tones from the POD® XT..." (http://line6.com/flextoneiii/ )

I don't speak about the (more or less) possibility to convert tones with the Line6Edit, but about the factory presets.

The Plexi Lead 100 factory preset differ even in the usage of the cab sim???

Plexi Lead 100    

Drv  Bas-Mid-Trb-Pre Vol

100 100-100-056-049 078 with 4x12 Brit T75 (Flexi)
075 100-082-100-067 056 with 4x12 Green 25's (PODxt)

Hiway 100

Drv  Bas-Mid-Trb-Pre Vol

087 091-085-035-039 043 with 4x12 Green 20's (Flexi)

087 059-051-100-084 039 with 4x12 Green 20's (PODxt)