I noticed the same thing but ... honestly, I don't think you have to worry about the exact scenario.
Your DC will play with the trains however your DC will play with the trains.
My DD has only seen a handful of Thomas episodes; she is very excited about the fact that they're trains, but it wouldn't occur to me to "encourage" her to play with her trains in any other way than the way she does.
She's only recently learned how to assemble the track pieces; I'd really be surprised if she had any idea that the show or stories were something she could also play at.
==========================================
Liz
DD (3/2010)
"Make mistakes! Get messy!" - Miss Frizzle