I think you somehow confuse two things:
One is the
charge (95%, mentioned by you), the other is the
battery health (97%, mentioned by the OP).
For example: The 2009 17" MBP has a battery capacity of 13,000mAh, if the charge is at 95%, there are still 12,350mAh of charge left.
If the battery health is reported as 97%, the maximum battery capacity is reduced to 12,610mAh, thus 95% charge of that capacity would be 11,980mAh.
It is true, the battery not always charges to 100% charge, but it normally does over time.