I think the answer lays in what and when you need access to the spikes.
If it is a pre-show thing, then you have lots of options (A grid, digital photos, building a cut out to lay on top of the deck with areas cut out, etc, etc)
If it is something an actor needs to see to put something down or hit a mark, then you are looking at a different situation - I would see if that section of gravel and sand be "PERMANENT" - glued down, and then you could lay down a spike, as long as that didn't disrupt the look or design.
If it is something that needs to happen during the quick change, and you light plot would open to it, I you could a special that is basically the spike that is projected down.
You can also be clever in how you sculpt the sand and rocks pre-show to make specific points.
We could come out with six or seven ways to do it . . . but with more specifics you could recommend a specific example.
I have had to do pre-sets before without any spikes, so you find cheats in the floor, take a lot of digital photos.
I did do a show in the sand last season, and for the actor spikes, we found ways (like be downstage of this brickwork, and just upstage of this boom.)