Just tested and it's working fine for me, the kit doesn't go through the ground when the time-warp is enabled as expected.
But there's some other problem I noticed, one that I think is easy to fix. The kit, when deployed from above the ground detaches from anything that it is attached to and waits some time until it stops moving, the problem is that it can stop its movement while still accommodating itself to the landscape, and then it deploys and gets fixed to the ground in an odd angle, what can cause it to "Launch" with some parts under the landscape, and making the physics of KSP just eject the vessel violently into the air, and some parts can blow up due to impact with the ground or stand upside down, which is bad. And I tested it on Kerbin, on the runway, so the problem may get worst when trying to deploy the kit in this such way on a body with a lower gravity.
So I think the mod should wait some seconds after the stop to verify again that there's no movement to then deploy the kit.