I found the bug; on line 41 and 42 of data/aquilo the code needs to be
local fluorine_vent_spread = " random_penalty{x=x,y=y,source=" .. "control:fluorine_vent:size}+(" ..
fluorine_vent_spread_source .. "control:fluorine_vent:size)"
instead of
local fluorine_vent_spread = " random_penalty{x=x,y=y,source=" .. "control:lithium_brine:size}+(" ..
fluorine_vent_spread_source .. "control:lithium_brine:size)"
This made it so that line 50 would set the spawn probability to zero if the map settings size of fluorine vents were smaller than the size of lithium brine.