As far as I can tell, MLFs have little to no basis in actual mass. That said, there is an overall trend of MLFs being bigger for ships that are physically larger and/or have more advanced systems.
Effectively, my head-canon is that ship MLFs are actually a measure of electronic interference given off by the ship rather than mass interference . A bigger ship with larger and more complex systems will give off more interference, resulting in a higher MLF.
I took the liberty of borrowing the ship data from Coriolis and plugging it into an excel spreadsheet, then made a few scatter plots of the various ships MLFs in comparison to hull mass and the sum of their module classes (core internals, hardpoints + utilities, optional internals, all of the above). While there is an overall trend for the hull mass vs. MLF plot, the correlation between mass and MLF is nowhere near as good as the correlation between the sum of module classes and MLF. For anyone who is interested, . Unfortunately, it wouldn't let me upload the excel file, so I had to copy everything to word. You will probably need to copy-paste everything back into excel to be able to see everything (I can confirm that this works).