Tented vias and / or soldermask over vias is optional but is generally recommended by PCB fabricators to prevent acidic and corrosive chemicals that are sometimes used during PCA assembly from being trapped inside the via, which could then result in circuit disconnects over time due to corrosion of the copper. Additionally, some of the vias in the design mentioned are located underneath the QFN components. The concern by the PCB fabricator for these vias is that solder can weep through the vias from the component side to the other side of the PCB and potentially create solder balls which can become dislodged and short circuit other exposed circuits.
To tent or to have solder mask placed on the vias in your design, simply place a fabrication note instructing your PCB fabricator to use either method for all exposed vias in the design.
To resolve this issue, we recommend you submit a technical support request at https://siliconlabs.force.com.
Thank you and best regards.