At many stations, the screens on the machines are so dim they are almost impossible to read - especially at certain times of the day when the sun's shining on them. The last time this happened to me (I couldnt buy a ticket because i couldnt see the text on the screen), i called Metrolink and they told me to "ask the conductor". So yeah, it's up to the conductor whether theyll let you on. Like someone else said though, loads of fare evaders try to claim the machines are down when in fact theyre working just fine, so what i would do is take a photo or video of all the machines so you at least have a little evidence they arent working. Dunno if that would help your case, but at least it's something.
I myself cant use the metrolink app as it apparently isnt compatible with my phone, but that's a good alternative option for others.
As for buying tix at the end of the line, at Union Station that would be a bit of a hassle as the only ticket machines (and a staffed Metrolink window where you can also buy tickets) are at either end of the station, requiring a long walk through the tunnel and back. I would just talk to the conductor next time and see what he/she recommends.