Actually, the altitude is a bit lower than that, as Interstate 90 crests the pass at 3,022 feet. The former Milwaukee right of way enters the east portal of the tunnel at Hyak, a couple miles east of the I-90 summit and, off the top of my head, probably closer to 2,700 feet altitude.
Bottom line is that the Milwaukee Road possessed the best route through the Cascades, even though they were the Jimmy Come Lately, well after Northern Pacific Railroad (not "Railway" until 1893) had surveyed (and rejected) Snoqualmie Pass and the Great Northern selected what became known as Stevens Pass.
Milwaukee also boasted truthfully of having the most direct route between Seattle and the Midwest, and was beating NP and GN times moving freight between Seattle and Minneapolis/Chicago.