Will using a PCB lacquer or any kind of thin conformal coating also have bad effects?
I would expect that it would interfere to some degree also.
The big thing is that you are going to then add another layer of a compound over the antenna traces that will add capacitance.
My solution on an ESP8266 module (sold as ESP-07) was as follows:
I designed the board to have a flat area in a rectangular path around the module and its decoupling capacitors.
I then used a small plastic enclosure with no lid, sold as a potting box.
The box measures about 37mm x 25mm x 12mm (1.5" x 1" x 0.5").
It is placed over the area to be protected from the potting compound and a small bead of silicone is used to glue it down
The module and its antenna are contained in 'free air' inside the box with no chance of silicone or potting compound coming in contact with it.
There are no vias in the board inside the potting box perimeter so that nothing can leak through from the other side of the PCB.
Being a custom designed board allowed me to make the rules...
Of course this is not going to be easy on a RPi board due to other component population, but you may be able to do something.
Keep all potting compounds away from the antenna traces and/or chip antenna.
Good luck.