Oh yes, for sure. I don't remember when maybe 8-15 years back, that was the EB's usual route. Thinking westbound #7, opposite of your route on #8, the Builder would hand-throw the switch out of MNNR at Saint Anthony park and take the sharp right-hand diverging route out of Saint Anthony Park junction on the MNNR northward less than a mile to Park Junction where they (and I) would see (Red over Green/Yellow) that put them on the ex-NP St. Paul Sub to Northtown.
That route - the one you took eastbound - has more freight - the Midway route that diverges eastbound from Northtown onto the old GN and into the MNNR yard and Amtrak Midway station is very little used since the CNW (UP) mostly quit operations at their (wrong name - but "Dinkytown"? "Union Yard", "Minneapolis" - something) yard.
So now, yes Amtrak almost always uses the ex-GN because there's little traffic on it late nights. And it interferes less with the busy double main. The BNSF Midway yard does most of its intermodal work daytimes, likewise the MNNR.
But the route you took is always an option. Which is faster? depends on traffic.
I think the route they mostly use now is a bit more scenic - you can see the "Witches Hat" - but it's usually dark anyhow.