Prepreg thickness: ECAD specs vs. fabrication result
The prepreg will give slightly, yes, but the exact amount is impossible to calculate. Generally manufacturers produce boards with thicknesses of +/- 10% of the nominal thickness, though that number will be higher for thinner boards. You will need to speak with your board fabricator to get a better idea of how the prepreg thickness varies.
Here is a table from Advanced Circuits illustrating the different prepreg types, and how much their thickness varies based on whether the adjacent copper layer is 30% vs. 70% filled.

Again, this is a rough illustration so take it with a grain of salt. The graphic comes from this pdf:
https://www.4pcb.com/media/prepreg-thickness-chart.pdf