However is correctly used in the example, with sense “To whatever degree”, that is, “no matter how much”. But it does not indicate whether the program's comprehensiveness outweighs its vintage. That could go either way. To specifically indicate one way or the other, sentences like the following can be used:
This program, while dated, is comprehensive.
This program, although comprehensive, is obsolete.
However comprehensive this program may be, it's obsolete.
The comprehensive scope of this program outweighs its dated status.
