In my experience it does not have to be a perfect 90-degree angle, so I wouldn't stress yourself into a railroad tracks phobia or anything. (I say that because that is the sort of thing I would do with that information, get so paranoid about hitting at exactly 90 degrees that I became terrified of crossing tracks at all.) You don't want to cross at less than a 45-degree angle or the thing you just described will happen, but you have a fair bit of fudging room between 90 and 45 degrees.

It happened to me once, on light rail tracks. I didn't fall or fly over the handlebars, and in fact I just thought I had a flat. It was easy to get the bike out, but it was really embarrassing.