Actually, I am not so sure if we should document "private" data types.
I would propose to change the score matrix tags from ```<Name>_``` to ```ScoreSpec<Name>```, e.g. ```Blosum30_``` to ```ScoreSpecBlosum30```. In the most cases the shortcuts ```Blosum30``` etc. are used for the score matrix definition, so the new tag naming is not to much exposed to the user.
You could use additional typedefs in order to ensure backwards compatibility, i.e.
```C++
typedef Blosum30_ ScoreSpecBlosum30;
```
On long term, we should discuss if the current shortcuts are extended to ```Blosum30Matrix``` to denote the actual score matrix and ```Blosum30``` as the naming for the tags. I suppose,  this would be more natural. 
Anyway, I am not aware of the 1.5 release state and to which extend backwards compatibility should be guaranteed.