I honestly hadn't heard of this being an issue. I now see that both Cannondale and Specialized recommend against spacers on top of the stem. Most of the guidance I've seen up to now is to run a spacer on top of the stem so that the stem clamp sits entierly on the steerer. I guess just do what the manufacturer says.

If possible, leaving the steerer a bit long is a good idea because it also give you more flexibility in using stems with taller stack heights as well as making the bike more resaleable.

In my experience, it's very hard to crack a steerer. I once tightened a stem down on a cut piece of steerer tube just to see how much it would take to crack the steerer. I ridiculously overtorqued it and wasn't able to get the steerer to crack. They are typically very strong, thick pieces.