Why? Because there was no point.
First, according to more modern astronomical measurements, the current length of the year is closer to about 365.2422 days, so they would've been relatively less accurate had they used a more precise value of 365.2425463 days per year.
Which leads to a very important point about math: you need to be very mindful about how much precision you actually have in your measurements.
Also, let's look at what that very modern document from NASA says:
Before contemplating further corrections to the Gregorian Calendar we
must consider how exact the value of 365.2422 is. The length of the average tropical year is now
more precisely 365.24219 days but it varies somewhat from year to year and does not track the
seasons precisely. Also, because of tiny orbital effects the average tropical year varies by about
.00005 days per 1,000 years. Thus correcting any error of this magnitude is probably a waste of
time.
That is not a new attitude. Most of the rest of this answer is based on this document. In it, we read about Copernicus:
Copernicus did not believe it was possible to have a perfect calendar, as the solar year was
too variable.
So even back then, there was a belief that the calendar would drift in a variable way making too detailed corrections pointless.
Now look at the some measurements that were taken in that era from page 19:
- 1252 Alfonsine 365.24254630
- 1543 Copernicus 365.24269676
- 1551 Prutenic 365.24719907
- 1574-75 Ignazio Danti 365.24166667
We can see pretty clearly that there wasn't a lot of agreement beyond a couple decimal points. As such, it is easy to see why someone might not bother to pay attention to that 0.0000630. They would see it as not a true reflection of reality, just an artifact of the imprecise math and in modern terms, well within the error bars.
It appears that the person ultimately responsible for the calendar was one Aloysius Lilius. From page 20, we see he came up with:
365 +1/4 – 1/100 + 1/400 + 4/100,000
which corresponds to the errors:
- minus 1 day every 4 years;
- plus 1 day every 100 years;
- minus 1 day every 400 years;
- minus 4 days every 100,000 years (that means minus 1 day every 25,000 years).
This was then the basis of the calendar with the last part dropped. We can easily understand why, though. It would not require any change from the Gregorian calendar in another 23,418 years!
At the time, the general view of the age of the Earth was in the thousands of years. In fact, the Alfonsine tables referenced in the question put it at 6984 BC. In addition, the general Catholic belief in the second coming of Christ gave a general expectation that there was an end date, and that it was at most hundreds or thousands of years away. If your worldview has the Earth lasting on the order of 10,000 years, why worry about 25,000?
So in summary:
- Their measurements weren't good enough to get that kind of precision required for a more accurate calendar
- They had reason to believe that the year was variable enough to make more precision impossible
- If the "best guess" was right, it would be trivial to fix on the year 25,000
- They had good reason (in their view) that the year 25,000 would not happen