The union that represents Metro train drivers has sought to take the company to the industrial umpire over its continued operation of a single X'Trapolis train – modified so it will not outpace the boom gates at level crossings – on the Frankston line.

The train has run up and down the line twice a day since October but has been re-engineered so it cannot accelerate at unsafe speeds. The X'Trapolis is the newest and fastest train type in Metro's fleet but only some of Melbourne's rail lines are equipped for it. At full acceleration, there is a risk that it could beat the signals that lower boom gates on the Frankston line's 30 level crossings.

The Frankston X'Trap is an easy target for the union, especially given the modifications made to ensure that it 'performs safely'. Given the current lack of political impetus to keep it running on the Frankston line, I am quite surprised that Metro continues running it.

The article is, not surprisingly, missing some facts.
Yes, the acceleration issue has been addressed by making it run like a 30 year old train. Some call that progress.
But there other problems at level crossings not related to acceleration which Metro is currently ignoring.

You could enlighten us on this other problem.

Currently this looks like the key issue

"The union and Metro are set to enter the bargaining period for a new enterprise agreement and face tense negotiations. The pay deal for Metro's 5000 staff expires on June 30 and the union wants an 18 per cent pay rise over three years."

Welcome to Union run Victoria.

On other lines there is enough room to creep forward just past the signal in order to activate the level crossing.
Some level crossings on the Frankston line, and the corresponding signal which protects them, are ridiculously close to where the train needs to stop at the platform.