The alternate base value is used as the calculation basis only, while the alternate calculation is used to modify the final value.
For example, imagine you have a condition type ZA01, with a condition record maintained (master data) for Rs100. Now, condition ZB01 also exists lower in the schema, but with a rate of 10%. The standard calculation would result in a final value of Rs110.
The alternate base value could say, "Don’t use Rs100 as the basis -- use the original price PR00 only, which was Rs90." Then, the final value would be Rs100 + (10% of 90) = Rs109.
The alternate calculation routine says, "ignore the 10% altogether. Instead, use an externally calculated 20%." Then, you end up with a final value of Rs100 + (20% of Rs100) = Rs120.