What is the morphology or etymology of the word 列车?
It's not a classifier here. From dictionary:

列车 lièchē
(1) [train]∶众多连续的车辆。一般指火车,尤指由牵引机车和运货或载客的车厢组成的连挂成列的火车

So you can see, 列 is short for 成列的 (lined up in a row), therefore it's put before 车 as an adj.