Thanks onlooker, looks great. I'd leave the top diode in though so that the 12V rail won't source current to the 28V input if it is disconnected or fails short or something.
As for ATX, the -12V rail is legacy and usually supplies less than an amp max. The +12V rail is where all the muscle is. In fact, many "enthusiast" supplies have a single 12V rail as the output of the main converter, and then hang smaller buck converters off that to make all the other ATX voltages. Motherboards and video cards draw the bulk of their power from the 12V rail and convert it to the needed voltage closer to the load. In any case, 24V still isn't enough to charge a 24V lead-acid battery.
Yes, the boost converter is controlled. I have voltage and current feedback, and the voltage is tapped from separate wires right to the battery terminals. I'm planning on doing "hysteretic" charging where it turns on until the voltage reaches a high-water mark, then shuts off until it hits a low mark. But it will be current limited both during a fast charge and float charge to keep the battery happy.