Does that always happen, and were there other eligible teams that would have done better?
Part of the issue there is that teams are selected from a modified "merge" of results from the California State meet rather than an actual regional race. That has two problems: first, you are comparing many more teams and makes it easier to have a team or two close to the top 2 teams, and also comparing different races on the same day means that it isn't a head-to-head comparison and one race might have simply been faster than another due to circumstances (e.g. heat, wind, pacing/crowded course, mud or torn up ground if it was raining, etc.). Was Glendora really the third best team that year or even that day? That's probably pretty debatable.
The other part is whether 17th is really worse than what others might have done if given the chance.
Glendora soundly beat AQ teams from New York and Heartland regions.
Glendora was roughly on par with an AQ team from the Northwest (Jesuit), Southeast (St. Albans DC) and South (Bridgeland TX).
That suggests the only regions that MIGHT have had clearly better teams were the Southwest, Northeast and Midwest. The Southwest already had 2 At-Large bids so they weren't eligible for more. So the question would be Glendora vs. Ridgefield CT and Plainfield North IL. Just looking at the results and assuming conditions were good and the courses haven't changed much in the last few years, I would assume Glendora's CA State race was better than either of those teams. A team time of 77:12 at Woodward Park should be somewhere around a 77:45-78:00 at La Verne Gibson (NXR Midwest) and around a 81:10 at Bowdoin (NXR Northeast). Ridgefield CT ran about 83:00 and Plainsfield North IL ran 79:10.
Just going off of NXN results and the NXR results of those 3 teams, it doesn't seem like Glendora's At-Large selection was that off. Of course, not everyone ran well at NXN and the NXR courses might not have all been in good condition or might have changed a little in the last few years, but it doesn't look unreasonable to me.