Electronic – How to calculate the maximum output power

The 5V rail will most definitely be able to supply the power that you need in your setup. For most ATX PSUs, the +5v rail has the largest current capacity of all rails on the supply. Many, if not most devices will charge as soon as there is a voltage applied to their USB port, so I'd say that aspect of your setup is also good. I wouldn't worry about a device overdraw; the current control is generally built into the device rather than the charger.

The only thing to really consider is similar to what you mentioned in your question; some devices will begin to charge at say, half of their current capacity, and only ramp up to full current once they've received some data from the charger/host device. But, this is only really an inconvenience, and most devices will charge with at least some initial current. The only device I can think of off the top of my head that won't charge at all without this enumeration is a Sony PlayStation 3 controller (but I'm sure there are more).

The final point is that this really just varies on a device to device basis. Some devices will charge with max current right off the bat, a few will be limited to initial max current, and a couple might not charge at all.

IMO the two main question would be :

1) What microcontroller do you use? You might be able to use it at a lower voltage, maybe by decreasing the clock frequency. This would simplify your problem a gread deal.

For example if you want to use an ATMega, you may power it with as low as 1.8V if you keep the clock frequency at or below 4MHz. It will also be happy at 8MHz with much less than 3.3V. Then you can power it straight from the battery/power manager chip; not using a regulator at all will give you some significant battery gains.

2) What is the 3V3 part's lowest rated voltage? Depending on that, and the possible gains you'd make by not regulating the mcu voltage, you may be able to just discard the last drops of juice from your lipo for the same battery life (there is not that much energy left when it drops below 3.3V anyway... plus, that'd be healthier for the battery), and get rid of the step-up to 3.3V altogether. Now a LDO regulator might to the job. No switching regulator means less noise ; less parts, less power usage, less volume/weight and less price also might mean a possible bigger battery...

In order to make the right choices you'd need to specify the specifications of the parts you'd use. But using an unregulated voltage for most of the circuit, including MCU, and regulated voltage for only the 3.3V parts has many advantages.