I've done both, and am happy to see a question that I can answer based on experience rather than speculation.
If you keep your BCS in first gear so that you move slow but have flail RPMs high, you can mow over them and chew them up. As noted above, the heavier ones may cause the knives to bounce back out of the way, and the design of the Berta is such that when they do so this in some places they collide with the knives behind them (on the 34" model, at least). So if you don't have too many saplings or aren't too worried about knife condition you can just mow over them. I'm generally become more willing to do this as the knives/sides are nearing the point where I'll need to replace them. If you have an older set lying around you might sharpen them, put them back on, and use them for this purpose.
You can cut them with a brush cutter, but will have to be careful about ensuring that they are cut flat. A pointed sapling stump is a bad thing to have on a road.
Also worth considering: Red alders have notoriously weak and shallow root systems (here near Seattle, at least) and after a good rain you might be able to pull them up or drag them out with a field cultivator or similar. If you have a second set of hands to help, you could put a choker chain around them and pull them out with the BCS. I've pulled out Blackberry roots with my BCS like this, and those buggers are tenacious. You could possibly combine the three techniques to good effect.