Bryan,
I have considerable experience of non-submersible offshore transport barges but the intent with those was always to keep them above water and to that effect ballast plans for the loaded condition were always checked and independently double-checked before approval.
First generation semi-sub cargo barges were non self-propelled and had fairly basic ballasting systems often using pumps for ballasting and pumps/compressed-air for deballasting but they did not submerge to quite the extent that the Super and Mighty Servant Class vessels do. The later vessels became bigger, self-propelled and able to submerge further but - as far as I am aware - ballasting systems remained fairly low-tech.
The big semi-sub, twin-hull, crane vessels used offshore with lift capacities ca. 20,000 ton have very sophisticated, high-capacity, ballasting systems which are computer controlled to provide rapid reaction to the application of big hook loads. I put this info in here because I wonder if something similar, although not as sophisticated, may be in use on the current generation of semi-sub barges.
As you would expect, the residual buoyancy in the semi-sub barges lies partly in the submerged stern of the barge, fine-tuned to stop it going right down (supplemented by the demountable tower tanks fitted aft when this does not interfere with the cargo) and the forward accommodation/machinery/bridge tower structure. A delicate balancing act that I'm glad I never had to cope with.
Some heavy-lift semi-sub jobs converted from tankers retain the aft superstructure and foc'sle and use side-loading, Thus I would expect these to retain far better stability and reserve buoyancy than the all-for'd types.
Does this help?
Cheers,
Barry M