OE's try to keep their systems (& black boxes) proprietary.
Although these ECU's often have a means of repflashing (EEPROM types) the ability is typically left to the OE dealerships (who can reflash updates & revisions to the software only). No changes or adjustments can be performed other than the odd factory option configurations.
Some tekkies have/can determine protocols and hack systems (this changes the software checksum as has been mentioned here).
Ease of use and the broad abilities to Map fuel, timing & output (eg.boost) controls have brought aftermarket user programmable ECUs into existance.
Racing relies on them.
Mods become far easier to see to completion.
Research the mods (from their manufacturer and blogs like this one). If calibration tuning is a recommended part of the full mod, you know what to do.