That seems unlikely. Surely the modem chip is connected to the 3V3 rail, not directly to the battery.
Modem modules are usually directly connected to the battery because 2G may draw too much energy during transmission pulses. Otherwise one would need a 3.3V regulator that can handle 2-3A pulses and still have no significant energy loss.
In the Pyra there is a 3-way switch in the charger chip. It negotiates energy flow between battery, usb power, and system (modem, omap5, display etc.).
The modem is connected to the system voltage rail which is just a little lower than battery voltage during discharge. This is important to keep the system running at low battery level.
During charge the system voltage can be up to 100mV above battery voltage (so that energy flows into the battery).
Now, for LiIon batteries charging has to stop at 4.2V.
But the Modem sends an overvoltage message at 4.25V and turns itself off.
Since it gets a 100mV higher voltage than the battery, the modem will turn off when the battery is full (or can't be turned on).
To avoid this we have to stop charging at 4.1V which is ca. 80% fuel level. And the fuel gauge chip and kernel drivers are not aware of this and report 4.1V as 80%.
So yes: the battery is not full (with some reserve for the modem not to turn off during charging). But it is as full as it can be.
Why was it designed as it is? Well, we were not aware of this 4.25V turn off point and the 100mV addition when we designed this and it was too late for a hardware modification (which would have been fundamental).