This is going to be a bit of a long post so sorry in advance hahahaha.
No, the documentation for it is a little weird, but alternate samples just changes the incoming midi velocity to any new number in a set round-robin range. This range is big enough that sometimes the new velocity output for the kitpiece will trigger a new sample layer, and might sound incorrect by being too loud or too soft compared to the intended velocity you had in mind. Turning it off leaves the midi velocity to stay the same as the input within the engine, which allows you to trigger the samples and velocity layers you want in a linear way.
There's only one sample per velocity number, and within each layer, every sample is similar but slightly different in volume and pitch (absolutely every sample is, I actually just went through cataloguing what the dB output and other differences were last night.) I got pretty tired of praying the playback of the notes would be correct on bounce/export, so I wanted to see what I would be missing with alternate samples turned off. Thankfully you don't lose anything unless you're kind of lazy and write/play midi at a fixed velocity, or copy and paste the same midi across the project without changing it slightly from the original. If you do, leaving alternate samples on is an easy way to get varying performances out of the same midi data, and might help you come up with a groove faster depending on how you write/record.
You can test this yourself by clicking the "?" on the GUI and opening the map window: with it on, whatever velocity coming in may or may not change on every other hit depending on the engine's round-robin. Using the same velocity will show you how big the round-robin range is, and give you an idea of what that velocity will sound like when in your project. With it off, the velocity will be the same as the input and trigger only the one sample, but that sample will be the exact same one that would be triggered under alternate samples if you got lucky and the velocity didn't change.
Velocity layers for kick drums at least, change after every 8/9/10 velocity amounts which leaves you with quite a bit of different layers to work with. For the kick drum I tested on, it seemed like somewhere in the lower middle, there was no big apparent sample layer switch. I've read somewhere once that other drums/cymbals have fewer or more velocity layers compared with each other (e.g. snare compared to hi-hat,) but I haven't checked to see if that's true or not, and whether or not any specific kitpiece is mapped differently.