Cooking, and what heat costs you
Updated
Every minute the sauce is hot buys you something and costs you something else. Knowing which is which is most of the craft in production.
What heat is for
Softening peppers so they blend smooth. Driving off water to reach the viscosity you want. Melding, which is real and not mystical: cooking moves a mixture from tasting like its parts to tasting like one thing.
And, where the process calls for it, reaching fill temperature.
What it takes away
Aromatics first. The fruity top notes of a habanero are volatile and they leave in the first serious simmer. A sauce built on those aromatics should be cooked briefly or have them added late.
Color next, which dulls steadily with time at temperature. Then freshness generally: a long-cooked sauce tastes cooked, which is a legitimate style and not the same product as a bright one.
Heat itself is unaffected. Capsaicin does not cook off, so a long reduction concentrates it as water leaves.
Order of operations
Cook what needs softening, add what needs melding, and hold back what you want to survive. Fresh aromatics, delicate peppers and some acids are better added near the end.
Acid timing matters for more than flavor. Your scheduled process specifies when acidification happens and how long equilibration runs from that point, so moving the vinegar earlier or later is a process change rather than a preference.
Cooking to a number
Time is the least reliable instrument in the kitchen because it does not know your pot, your burner or your volume. Cook to weight or to a viscosity check instead.
Weighing the pot is the cheapest control available: note the target finished weight, and reduce until you reach it. It survives scaling, it survives a different stove, and it is the single change that does most for batch-to-batch consistency.