When using the MegalowPartsFix option, the discount for packages is the standard 10% instead of the 20% it is intended to be for Megalow. The option for Stage 3 upgrades is also visible, which it is not supposed to be.
MegalowPartsFix = 1

MegalowPartsFix = 0

I'm also not observing what the fix is supposed to otherwise do, I'd be interested in seeing what difference I'm missing.
That being said, without these two issues being fixed I would probably suggest changing the default setting in the ini to MegalowPartsFix = 0