I'm wondering if there was a modification made to the PROM from GM
It's possible. But any calibration GM releases for domestic use needs to have EPA approval. Making a change for only one chip is a big project and releasing a chip without EPA testing and approval can result in massive fines.

Here's a thought provoker: The file on the chip contains a checksum. The checksum is a value that is derived using an equation applied to all the bytes in the chip. The ecm looks also at all the bytes in the chip does the same calculation, then checks its results against the checksum stored on the chip. If a byte is changed in the file, the checksum doesn't match and the ecm sets a code for an eprom error.

The checksum in your chip does not match the one that results from applying the formula to all the bytes in the chip.

Since you haven't reported that your ecm is setting a code for eprom error, either the checksum calculation in the software I'm using is incorrect or the data in the file does not match the data used for the original checksum calculation. I have used three different programs to confirm the checksum is wrong and I highly suspect that all three are in error. Therefore I suspect the data in the file presented does not match the data in the chip. I.E., a bad read.

Unfortunately I have no experience with Flash & Burn to advise. But I do suspect the five speed equipped 4.3Z calibration is easily locatable using Hen's Tooth extract mixed with a drop of liquid Unobtainum.