Bob,
I am in Norfolk with clients the week after next - possibly the same unit as you.
Firstly, the amounts mentioned (250/50k) are the annual amounts that you once could/ now can put into your pension fund each year before incurring tax. In the case of mil, its a nominal amount allocated by the MoD for you and not what you put in yourself.
The amount that you mentioned commuting is tax free and there is no suggestion that the State is going to change that. You can invest it as you wish, or place that into an other pension fund to gain further tax relief if you are still earning and don't need it immediately.
Hope that helps.