I suspect you will struggle to get a definitive answer but I offer the following thoughts.
- Power electrical distribution design typically assumes loads will have a distribution of power demands, both in maximum demand values and demand varying with time. e.g. some power sockets in your home will have a light load such as TV or light, others near maximum power rating like a washing machine or electric heater. If you were load all of the sockets with loads near the maximum rating at the same time, you will probably trip the home circuit breakers. This is not a design fault - it is a sensible compromise knowing the typical usage with reasonable margin. It is not unusual to see the (simplistic) total socket output rating being 4 (or more) times that of the supply circuit capability.
- Your motherboard is also home to the processors, memory, etc. of your computer. Running high currents across it will tend to introduce voltage drops, noise, temperature rise, etc. These all reduce reliability.
- Consider your power supply which must also meet all demands of processor and drives.
In summary, I don't design motherboards, but if I did, I would not expect all USB ports to be continually running at near their maximum load. By contrast, digital electronics will often do its best to carry on working, even under fault and bad design conditions. My rough guess is that it will attempt to work, but suffer 'unexplained' crashes. If you want a reliable system, look for a better scheme providing the hard drive power from an independent source.
And in answer to 'Why might the motherboard not support full current on all ports at the same time?' The PCB tracks and planes are made of copper, which has a resistance. High current flow means voltage drops across that resistance. The designer can reduce the resistance by using thicker copper layers, but that increases cost and weight. Motherboards must be competitively priced - if only 1 in 100,000 customers need a more expensive option, do you think it will be included? - Especially if it doesn't provide a 'very attractive' extra selling point. Most USB loads are quite low current, so requiring a maximum current on the whole set simultaneously is unusual. Estimating the realistic total load and designing an appropriate solution in this way is part of the normal work for a power distribution engineer. As I said above, it might 'just' work but don't be surprised if it crashes from time to time.
Or do motherboards normally have a total max, e.g 3A, 4A, 5A etc?
I think that's at least true for "boards" like Raspberry Pi. But on a PC I can't think of a reason for a motherboard not to allow/guarantee that all of its USB ports to provide the spec max simultaneously.