Well, good news everyone. I found a way to make flooding weight affect the boot on the surface.

Now heavy flooding weight will pull the boot back down below the surface. Also, the boot will now founder on the surface while cruising with medium to heavy flooding. Underwater affects and weights from flooding are not affected! I will try to include this feature in the next release of LRT.
Below is a pic from the testing I am doing. The boot has half of the bow torpedo room flooded. Surface speed is greatly reduced due to submerged drag. The boot will sink soon.