A fairly regular question this.
XC in the Midlands is an easy one to answer, originally the core long distance XC (without the former Central Trains services) didn't call anywhere that didn't also have a local TOC calling as well. With the additional routes being of a slightly different nature they suddenly became the sole callers at randomly located and relatively minor stations. The small number of stations does not justify XC having a property management set up, and there wouldn't be sufficient critical mass to employ dedicated station staff and run the necessary training and management. So the 2007 franchise explicitly ruled out XC taking over these few stations.
The two stations mentioned that SWT now make all the calls at (Dean and Mottisfont) were supposed to be transferring to SWT - it was covered in the 2012 FGW franchise ITT which was subsequently abandoned, and it would appear that DfT have forgotten about it.
There are many edge cases around the country where the TOC with the most services doesn't necessarily run the stations, take Swanwick near me as an example, where Southern make twice as many calls as SWT, but it's well off SN's normal patch, so I doubt anyone would ever consider it needed changing. I suppose you could say the same about Romsey - it's out of FGW's main area, and SWT make more calls there as well...