Sketch Size Changes due to Arduino being Uploaded (Uno R3 vs. Fio V3)

I have an Arduino Uno R3 and Fio V3 which will both have an MPU9150 attached. I have found library and 9 Axis Data Fusion provided athttps://github.com/richards-tech/MPU9150Lib by richards-tech. There is a calibration sketch (MagCal9150.ino) and a sample sketch which I would like to use. From my understanding, both the Uno and Fio have 32K Flash memory. However, I have different experience when going to upload to one vs the other.

For the Uno, when I Verify MagCal9150, all is well, with the following displayed ..
Binary sketch size: 28,706 bytes (of a 32,256 byte maximum)
So there is no issue, however I am confused with it come to the Fio V3 as I get this error on Verify...
Sketch too big;
Binary sketch size: 31,312 bytes (of a 28,672 byte maximum)

This confuses me for two reasons...
The sketch size increases by ~3K
The max sketch size decreases by ~3K

That's 3K difference on both ends that I cannot explain... Any clues? thanks in advance!

From my understanding, both the Uno and Fio have 32K Flash memory.

They do, but they have different bootloaders (with different sizes) and different means of communicating with the PC. That difference means less room for your sketch on the FIO.