Maybe I didn't explain well, but this isn't the assumption the calculator is making. By three months old, I'm talking about the production date on the calculator, which is referring to the age of the vial according to the tool tip.
Once you've poured the first vial into a starter, its age is categorically irrelevant. That starter is producing new, healthy yeast, and the yeast from that starter have good healthy glycogen stores. EDIT: to be clear, as long as you let the yeast completely finish out the starter wort, the strongest factor in how many yeast cells you get from a starter is its volume. Since the yeast are approximately doubling in each generation, the final generation uses at least as much energy to multiply as the sum of all generations before (since the sum of 2^k for k from 0-(n-1) is (2^n)-1). Thus, the volume of the starter determines your final cell count to within a factor of two, which is as good an accuracy as you can expect without doing dilutions and cell counts.
Let's say that today you have a WLP vial that is 6 months old. You dump that into a 1L starter, and in a few days you have ~150B "young" cells (age=0). You split this up into five jars, J1-J5, 30B cells each. The age of these jars starts counting from today.
In one month, you decide to use J1. It's got ~23B cells in it (75%), which is on the low side for pretty much any 5gal batch, so you make a 1-2L starter (depending on gravity) and you're off.
The next month, you're busily brewing, and you make three more batches. J2-J4 all have ~15B viable cells (50%), so you make a new starter for each and pitch.
In the third month, you use your last jar, J5. This one, being three months old, has an estimated 10B viable cells (33%)---still enough to make a 1L starter according to the 1 million cells / degree plato / mL guideline.
If you had waited until the fourth month, and decided to brew a high gravity beer requiring a 2L starter, you'd be starting with only ~7B cells (25%), so instead of jumping straight to a 1L starter as your first step (which honestly would be OK), you'd make a 500mL starter and then step that up into a 2L starter before pitching.
In summary: what matters is the time since the yeast last had the ability to replenish their glycogen stores. The stuff you pull out of a starter is "new" for the purposes of the pitching rate calculator.