As of version 5.0.0-rc2 (commit 93c7f65d to be precise), there is a change in way the solder mask and solder paste clearances are determined. For pads defined with copper layers, the solder mask and solder paste clearance calculations remain the same. For pads defined with no copper layers (referred to as aperture pads), the inherited clearance and ratio settings are no longer applied and the pad is plotted as defined. This was done to allow for complex and accurate mask and paste layer generation without requiring changes to the existing file format and not requiring the KiCad footprint libraries to use extremely small clearances and/or ratios to prevent the board and footprint level clearances from being applied to the solder mask and solder paste layers. If you have any existing aperture pads defined in your boards, please be aware that the next time you plot them, they will not have the clearance settings applied to them.
Thank you for your patience during this transition.
The KiCad Development Team