The Cobalt includes two algorithms. The "folded" RGBM covers shallower dives and has safety stops near the surface (±3m) that can be ignored with no repercussions. In deco, this algorithm can also incorporate a half max depth/ Pyle stop, depending on the max depth reached and the ascent profile generated. Atomic, in conjunction with the algorithm designer, decide that they would treat this stop as a deco stop, so violating it would create the same alerts and flags as a missed deco stop. This was a decision made by Atomic based on their understanding at the time, and you are correct in that there is no provision in the firmware to disable this stop. There is no lock out, so if you page through the alerts, the Cobalt will continue to work and calculate normally, albeit displaying a warning.
If your max depth is deeper than about 150' / 45m the "fully iterative" RGBM algorithm takes over, and you will see an ascent profile that typically has short stops every few meters.
From what you say, I'm not 100% sure which scenario fits your dives, but I"m guessing the folded algorithm if you are seeing something that looks like a Pyle stop.
We are no longer associated with Atomic / Huish and they pulled the plug on Cobalt, so updates to the Cobalt's firmware are no longer happening. If they were, we would certainly recommend modifying this feature to be at minimum optional, or eliminate it altogether. But we are/ were not the algorithm designers, so it would not ultimately be our call.
In our future independent products, we do not incorporate this stop, and also provide the option of switching between RGBM and a Haldane algorithm.
Sorry I don't have a better solution.
Ron