1. How come such as busy franchise as XC with packed trains apparently makes a loss?
Because they are packed not because it's so popular but because the trains are so small.
A Class 220 for example seats 174 people in standard.. Whereas an XC HST seats 389 people in standard. The standard class capacity of a Voyager is just 2 passengers more than a 3 car Class 159.
If you put 200 people on a 220 then its 'packed' but if you fit those same 200 people on an HST it's half empty, yet the 'popularity' of the service is the same in both scenarios. The Voyager is, despite how much we hate it, an 'Intercity' train and carries operating costs commensurate with this sort of train but simply doesn't carry enough passengers to generate significant contribution to running costs.
XC is busy because it has pathetic capacity levels per train not because it's got so many fare paying passengers. The same passenger loadings on properly lengthed IC trains would feel empty even at peak times..
It's a bit of a vicious circle, XC fares are notoriously high, even many of the Advances on offer are often barely cheaper than a walkon, as a result of the limited capacity. They can't cut fares because there is no capacity for the extra passengers they'd get. But if they were to increase capacity it would take a long time for consumer confidence to return to a level whereby they could increase passenger volume to fill the larger trains by enough to generate significantly more revenue.
Putting an extra HST on sadly doesn't generate more cash - most people who don't travel XC but might if they didnt expect a Voyager crush still wouldnt want to risk it.
Therefore the HST's are seen purely as a cost to the business, hence being used spareingly.